Name: Garciella nitratireducens DSM 15102
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5451

Type strain:

Species: Garciella nitratireducens

Culture col. no.: DSM 15102, CIP 107615, MET 79

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

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

SI-ID 97650

CIP 107615, DSM 15102

Special Collections

DSMZ
CIP

Section

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

spore-forming
anaerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Eubacteriaceae*
	Genus	*Garciella*
	Species	**Garciella nitratireducens**
	Full Scientific Name (LPSN)	Garciella nitratireducens Miranda-Tello et al. 2003

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5713]

Culture medium

DESULFOBACTER MEDIUM (DSMZ Medium 193)

[Ref.: #5713]

Culture medium growth

[Ref.: #5713]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5713]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5713]			growth	55 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5713]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %92.276

[Ref.: #69481]

Ability of spore formation

yes Confidence in %100

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	purine metabolism	69.15	65 of 94
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	oxidative phosphorylation	57.14	52 of 91
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	55.56	5 of 9
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	lysine metabolism	42.86	18 of 42
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	non-pathway related	39.47	15 of 38
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	lipid metabolism	35.48	11 of 31
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	pentose phosphate pathway	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	25	3 of 12
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	toluene degradation	25	1 of 4
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #5713]	Sample type/isolated from	separator tank
[Ref.: #5713]	Geographic location (country and/or sea, region)	Gulf of Mexico, Tabasco, SAMIII oilfield
[Ref.: #5713]	Country	Mexico
[Ref.: #5713]	Country ISO 3 Code	MEX
[Ref.: #5713]	Continent	North America
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Engineered product
#Engineered	#Industrial	#Oil reservoir

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY176772 (>99% sequence identity) for Garciella nitratireducens subclade from Microbeatlas

Aquatic Samples	12
Soil Samples	2
Animal Samples	19
Plant Samples	1
Total Samples	34

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #5713]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #5713]	Garciaella petrolearia strain Met 79 16S ribosomal RNA gene, partial sequence	AY176772	1471	GenBank ENA	218205 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Garciella nitratireducens DSM 15102	GCA_900167305	scaffold	GenBank ENA	1121911 tax ID	*
[Ref.: #66792]	Garciella nitratireducens DSM 15102 strain DSM 15102	1121911.3	wgs	PATRIC	1121911 tax ID	*
[Ref.: #66792]	Garciella nitratireducens DSM 15102	2568526006	draft	JGI IMG/M	1121911 tax ID	*

[Ref.: #5713]

GC-content

30.9 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Garciella nitratireducens DSM 15102 DSM 15102 NCBI: GCA_900167305.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Garciella nitratireducens DSM 15102 DSM 15102 NCBI: GCA_900167305.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	73.229	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	92.276	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	98.596	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	yes	62.989	no
[Ref.: #69480]	thermophilic	thermophileⓘ	yes	60.666	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	71.422	no

Availability in culture collections External links

[Ref.: #5713]

Culture collection no.

DSM 15102, CIP 107615, MET 79

[Ref.: #74939]

SI-ID 97650

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	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	*
Phylogeny	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	*

References

#5713

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15102

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#74939

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID97650.1 )

* These data were automatically processed and therefore are not curated

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Garciella nitratireducens DSM 15102 DSM 15102

Garciella nitratireducens DSM 15102 DSM 15102

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