Thioalkalivibrio denitrificans (DSM 13742, NCCB 100001, ALJD)

Name: Thioalkalivibrio denitrificans (DSM 13742, NCCB 100001, ALJD)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4286

Type strain

Strain Designation ALJD

Culture col. no. DSM 13742 NCCB 100001 ALJD

NCBI tax ID(s) 108003

Special Collections DSMZ

History DSMZ <- D. Y. Sorokin; ALJD

Links

Thioalkalivibrio denitrificans ALJD is a bacterium that was isolated from soda lake.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 101021

DSM 13742,NCCB 100001

@ref 20215

Last LPSN update 2026-05-29 08:25:54

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Chromatiales

Family Ectothiorhodospiraceae

Genus Thioalkalivibrio

Species Thioalkalivibrio denitrificans

Full scientific name Thioalkalivibrio denitrificans corrig. Sorokin et al. 2001

Synonyms (1)

Thialkalivibrio denitrificans

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98.494

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5140	ALKALIPHILIC SULPHUR RESPIRING STRAINS MEDIUM (DSMZ Medium 925)		Medium recipe at MediaDive	Name: ALKALIPHILIC SULPHUR RESPIRING STRAINS MEDIUM (DSMZ Medium 925) Composition: Na2CO3 20.0 g/l NaHCO3 10.0 g/l NaCl 5.0 g/l K2HPO4 1.0 g/l MgCl2 x 6 H2O 0.2 g/l H3BO3 0.0006 g/l CoCl2 x 6 H2O 0.0004 g/l ZnSO4 x 7 H2O 0.0002 g/l Na2MoO4 x 2 H2O 6e-05 g/l MnCl2 x 4 H2O 6e-05 g/l NiCl2 x 6 H2O 4e-05 g/l CuCl2 x 2 H2O 2e-05 g/l EDTA 1e-05 g/l FeSO4 x 7 H2O 4e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
5140	positive	growth	30

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		99.44

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	hydrogen production	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	photosynthesis	100	14 of 14
66794	cardiolipin biosynthesis	100	7 of 7
66794	coenzyme A metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	denitrification	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	threonine metabolism	90	9 of 10
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	NAD metabolism	83.33	15 of 18
66794	glycine betaine biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	lipoate biosynthesis	80	4 of 5
66794	heme metabolism	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	gluconeogenesis	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	purine metabolism	71.28	67 of 94
66794	glycolysis	70.59	12 of 17
66794	leucine metabolism	69.23	9 of 13
66794	urea cycle	69.23	9 of 13
66794	non-pathway related	68.42	26 of 38
66794	cysteine metabolism	66.67	12 of 18
66794	cyanate degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	lipid A biosynthesis	66.67	6 of 9
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	formaldehyde oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	alanine metabolism	65.52	19 of 29
66794	lipid metabolism	64.52	20 of 31
66794	glutathione metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	ketogluconate metabolism	62.5	5 of 8
66794	pyrimidine metabolism	62.22	28 of 45
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	methionine metabolism	61.54	16 of 26
66794	glycogen metabolism	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	histidine metabolism	55.17	16 of 29
66794	lysine metabolism	54.76	23 of 42
66794	pentose phosphate pathway	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	sulfate reduction	53.85	7 of 13
66794	lactate fermentation	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	vitamin E metabolism	50	2 of 4
66794	tyrosine metabolism	50	7 of 14
66794	tryptophan metabolism	47.37	18 of 38
66794	nitrate assimilation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	propanol degradation	42.86	3 of 7
66794	oxidative phosphorylation	42.86	39 of 91
66794	O-antigen biosynthesis	40	2 of 5
66794	degradation of sugar acids	40	10 of 25
66794	arachidonate biosynthesis	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	Entner Doudoroff pathway	40	4 of 10
66794	D-cycloserine biosynthesis	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	degradation of hexoses	38.89	7 of 18
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	degradation of sugar alcohols	37.5	6 of 16
66794	metabolism of disaccharids	36.36	4 of 11
66794	polyamine pathway	34.78	8 of 23
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	carotenoid biosynthesis	31.82	7 of 22
66794	phenol degradation	30	6 of 20
66794	arachidonic acid metabolism	27.78	5 of 18
66794	ascorbate metabolism	27.27	6 of 22
66794	vitamin B12 metabolism	26.47	9 of 34
66794	methanogenesis from CO2	25	3 of 12
66794	toluene degradation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	allantoin degradation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Condition	#Alkaline	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
5140	soda lake	Kenya	KEN	Africa

Taxonmaps

69479

Global distribution of 16S sequence AF126545 (>99% sequence identity) for Thioalkalivibrio denitrificans from Microbeatlas

Aquatic Samples	178
Soil Samples	16
Animal Samples	6
Plant Samples	4
Total Samples	204

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5140	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM200036v1 assembly for Thioalkalivibrio denitrificans ALJD	scaffold	GCA_002000365	2899100019	108003	22.64

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5140	Thioalcalovibrio denitrificans 16S ribosomal RNA gene, partial sequence	AF126545	1465		108003

GC content

5140

GC-content (mol%)63.7

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM200036v1 assembly for Thioalkalivibrio denitrificans ALJD
NCBI: GCA_002000365

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	59.15	no
125439	gram_stain	BacteriaNetⓘ	negative	81.54	no
125439	motility	BacteriaNetⓘ	yes	59.56	no
125439	spore_formation	BacteriaNetⓘ	no	99.44	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thioalkalivibrio denitrificans ALJD
NCBI: GCA_002000365.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	no
125438	anaerobic	anaerobicⓘ	no	73.12	no
125438	aerobic	aerobicⓘ	no	53.26	no
125438	spore-forming	spore-formingⓘ	no	89.61	no
125438	thermophilic	thermophileⓘ	no	93.70	yes
125438	flagellated	motile2+ⓘ	yes	78.77	no

Literature

Title	Authors	Journal	DOI	Year
Development of quantitative PCR for the detection of Alkalilimnicola ehrlichii, Thioalkalivibrio sulfidiphilus and Thioalkalibacter halophilus in gas biodesulfurization processes.	Kiragosyan K, van Veelen P, Gupta S, Tomaszewska-Porada A, Roman P, Timmers PHA.	AMB Express	10.1186/s13568-019-0826-1	2019

References

#5140	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13742
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

About us

Thioalkalivibrio denitrificans (DSM 13742, NCCB 100001, ALJD)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002000365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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