Thioclava dalianensis (DSM 29618, CGMCC 1.12325, LMG 27290)

Name: Thioclava dalianensis (DSM 29618, CGMCC 1.12325, LMG 27290)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130630

Type strain

Strain Designation DLFJ1-1

Culture col. no. DSM 29618 CGMCC 1.12325 LMG 27290 MCCC 1A03957 DLFJ1-1

NCBI tax ID(s) 1185766

Special Collections DSMZ Literature strains

History <- LMG <- Q. Lai, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China

Links

Thioclava dalianensis DLFJ1-1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from oil-degrading bacterial consortium, enriched by surface seawater.

Gram-negative rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 382321

DSM 29618,LMG 27290,CGMCC 1.12325

@ref 20215

Last LPSN update 2026-02-09 11:31:16

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Thioclava

Species Thioclava dalianensis

Full scientific name Thioclava dalianensis Zhang et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30859	negative	1.15 µm	0.75 µm	rod-shaped
125439	negative				99.3
125438	negative				98

Colony morphology

21842

Incubation period1-2 days

Pigmentation

30859

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21842	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21842	positive	growth	30
30859	positive	growth	04-37
30859	positive	optimum	28

Physiology and metabolism

Oxygen tolerance

30859

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		97.1
125438		90.362

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30859	NaCl	positive	growth	0.5-15 %
30859	NaCl	positive	optimum	3 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30859	30089 ChEBI	acetate	+	carbon source
30859	16449 ChEBI	alanine	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
30859	22653 ChEBI	asparagine	+	carbon source
30859	35391 ChEBI	aspartate	+	carbon source
30859	17057 ChEBI	cellobiose	+	carbon source
30859	16947 ChEBI	citrate	+	carbon source
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
30859	23652 ChEBI	dextrin	+	carbon source
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
30859	28757 ChEBI	fructose	+	carbon source
30859	33984 ChEBI	fucose	+	carbon source
30859	24148 ChEBI	galactonate	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
30859	24265 ChEBI	gluconate	+	carbon source
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
30859	17234 ChEBI	glucose	+	carbon source
30859	32323 ChEBI	glucuronamide	+	carbon source
30859	29987 ChEBI	glutamate	+	carbon source
30859	17754 ChEBI	glycerol	+	carbon source
30859	17596 ChEBI	inosine	+	carbon source
30859	17240 ChEBI	itaconate	+	carbon source
30859	21217 ChEBI	L-alaninamide	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
30859	24996 ChEBI	lactate	+	carbon source
30859	17716 ChEBI	lactose	+	carbon source
30859	25017 ChEBI	leucine	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
30859	15792 ChEBI	malonate	+	carbon source
30859	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
30859	37684 ChEBI	mannose	+	carbon source
30859	28053 ChEBI	melibiose	+	carbon source
30859	51850 ChEBI	methyl pyruvate	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
30859	28044 ChEBI	phenylalanine	+	carbon source
30859	26271 ChEBI	proline	+	carbon source
30859	26490 ChEBI	quinate	+	carbon source
30859	16634 ChEBI	raffinose	+	carbon source
30859	26546 ChEBI	rhamnose	+	carbon source
30859	15963 ChEBI	ribitol	+	carbon source
30859	17822 ChEBI	serine	+	carbon source
30859	30911 ChEBI	sorbitol	+	carbon source
30859	30031 ChEBI	succinate	+	carbon source
30859	26986 ChEBI	threonine	+	carbon source
30859	17748 ChEBI	thymidine	+	carbon source
30859	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
30859	16704 ChEBI	uridine	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
30859	acid phosphatase	+	3.1.3.2
30859	alkaline phosphatase	+	3.1.3.1
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
21842	catalase	+	1.11.1.6
30859	catalase	+	1.11.1.6
30859	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
21842	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
30859	urease	+	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ppGpp biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	L-lactaldehyde degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	valine metabolism	100	9 of 9
66794	resorcinol degradation	100	2 of 2
66794	butanoate fermentation	100	4 of 4
66794	octane oxidation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cellulose degradation	100	5 of 5
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	gluconeogenesis	100	8 of 8
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	vitamin B1 metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	pentose phosphate pathway	81.82	9 of 11
66794	tryptophan metabolism	81.58	31 of 38
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	heme metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	urea cycle	76.92	10 of 13
66794	vitamin B12 metabolism	76.47	26 of 34
66794	CMP-KDO biosynthesis	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	degradation of sugar alcohols	75	12 of 16
66794	ketogluconate metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	lactate fermentation	75	3 of 4
66794	pyrimidine metabolism	73.33	33 of 45
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	tyrosine metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	lipid metabolism	70.97	22 of 31
66794	methionine metabolism	69.23	18 of 26
66794	lysine metabolism	69.05	29 of 42
66794	purine metabolism	68.09	64 of 94
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	cyanate degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	non-pathway related	65.79	25 of 38
66794	phenol degradation	65	13 of 20
66794	oxidative phosphorylation	64.84	59 of 91
66794	glycolysis	64.71	11 of 17
66794	vitamin B6 metabolism	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	3-chlorocatechol degradation	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	degradation of sugar acids	60	15 of 25
66794	myo-inositol biosynthesis	60	6 of 10
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	propanol degradation	57.14	4 of 7
66794	glutathione metabolism	57.14	8 of 14
66794	degradation of pentoses	57.14	16 of 28
66794	cysteine metabolism	55.56	10 of 18
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	polyamine pathway	52.17	12 of 23
66794	histidine metabolism	51.72	15 of 29
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	pantothenate biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	propionate fermentation	50	5 of 10
66794	degradation of hexoses	50	9 of 18
66794	glycine metabolism	50	5 of 10
66794	quinate degradation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	sulfate reduction	46.15	6 of 13
66794	d-xylose degradation	45.45	5 of 11
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	ascorbate metabolism	40.91	9 of 22
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	starch degradation	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	metabolism of disaccharids	36.36	4 of 11
66794	sulfoquinovose degradation	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	chlorophyll metabolism	33.33	6 of 18
66794	coenzyme M biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
21842	-	-	-	-	-	+	-	+	+	+	+/-	+	+	+	+	-	+/-	+	+	+	+
21842	-	-	-	-	-	+	-	+	+/-	+	+/-	+	+	+	+	-	+/-	+	+	+	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Laboratory	#Lab enrichment
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water
#Host	#Microbial	#Bacteria

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21842	oil-degrading bacterial consortium, enriched by surface seawater	Dalian Port	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence JQ844756 (>99% sequence identity) for Thioclava dalianensis subclade from Microbeatlas

Aquatic Samples	416
Soil Samples	27
Animal Samples	15
Plant Samples	6
Total Samples	464

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21842	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2663762756 annotated assembly for Thioclava dalianensis CGMCC 1.12325	scaffold	GCA_900115035	1185766.6	2663762756	1185766	70.54
66792	SOAPdenovo v1.05 assembly for Thioclava dalianensis DLFJ1-1	contig	GCA_000715505	1185766.4	2585427678	1185766	60.04

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21842	Thioclava dalianensis strain DLFJ1-1 16S ribosomal RNA gene, partial sequence	JQ844756	1435		1185766
124043	Thioclava dalianensis strain DLFJ1-1 16S ribosomal RNA gene, partial sequence.	KX618931	1432		1185766

GC content

30859

GC-content (mol%)62.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Thioclava dalianensis CGMCC 1.12325
NCBI: GCA_900115035

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.10	no
125439	motility	BacteriaNetⓘ	yes	72.20	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	81.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thioclava dalianensis CGMCC 1.12325
NCBI: GCA_900115035.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	yes
125438	anaerobic	anaerobicⓘ	no	91.88	yes
125438	aerobic	aerobicⓘ	yes	82.73	no
125438	spore-forming	spore-formingⓘ	no	90.36	no
125438	thermophilic	thermophileⓘ	no	97.49	yes
125438	flagellated	motile2+ⓘ	yes	71.83	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	A Multilocus Sequence Analysis Scheme for Phylogeny of Thioclava Bacteria and Proposal of Two Novel Species.	Liu Y, Lai Q, Shao Z.	Front Microbiol	10.3389/fmicb.2017.01321	2017
Phylogeny	Thioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments.	Chang R, Bird L, Barr C, Osburn M, Wilbanks E, Nealson K, Rowe A	Int J Syst Evol Microbiol	10.1099/ijsem.0.002723	2018
Phylogeny	Thioclava nitratireducens sp. nov., isolated from surface seawater.	Liu Y, Lai Q, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001844	2017
Phylogeny	Thioclava indica sp. nov., isolated from surface seawater of the Indian Ocean.	Liu Y, Lai Q, Du J, Xu H, Jiang L, Shao Z	Antonie Van Leeuwenhoek	10.1007/s10482-014-0320-3	2014
Phylogeny	Thioclava atlantica sp. nov., isolated from deep sea sediment of the Atlantic Ocean.	Lai Q, Li S, Xu H, Jiang L, Zhang R, Shao Z	Antonie Van Leeuwenhoek	10.1007/s10482-014-0261-x	2014
Phylogeny	Thioclava dalianensis sp. nov., isolated from surface seawater.	Zhang R, Lai Q, Wang W, Li S, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.046094-0	2013

References

#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 )
#21842	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29618
#27189	IJSEM 2981 2013 ( DOI 10.1099/ijs.0.046094-0 , PubMed 23378112 )
#30859	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27189
#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 )
#68369	Automatically annotated from API 20NE .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

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Thioclava dalianensis (DSM 29618, CGMCC 1.12325, LMG 27290)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900115035

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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