Thioclava pacifica (DSM 10166, UNIQEM 229, TL 2)

Name: Thioclava pacifica (DSM 10166, UNIQEM 229, TL 2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13804

Type strain

Strain Designation TL 2

Culture col. no. DSM 10166 UNIQEM 229 TL 2

NCBI tax ID(s) 1353537 285109

Special Collections DSMZ Literature strains

History DSMZ <- D. Yu. Sorokin; TL 2

Links

Thioclava pacifica TL 2 is an aerobe, Gram-negative, motile bacterium that was isolated from sulfidic thermal sea water.

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

Name and taxonomic classification

SI-ID 139011

DSM 10166

@ref 20215

Last LPSN update 2026-05-29 08:28:08

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Thioclava

Species Thioclava pacifica

Full scientific name Thioclava pacifica Sorokin et al. 2005

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31370	negative	rod-shaped
125438	negative		97.8
125439	negative		91.959

Colony morphology

3837

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3837	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)
3837	positive	growth	28
31370	positive	growth	15-47
31370	positive	optimum	35

Culture pH

@ref	Ability	Type	PH	PH range
31370	positive	optimum	8
31370	positive	growth	6.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

31370

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125438		91.14
125439		96.935

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31370	30089 ChEBI	acetate	+	carbon source
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
31370	16449 ChEBI	alanine	+	carbon source
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
31370	22653 ChEBI	asparagine	+	carbon source
31370	17057 ChEBI	cellobiose	+	carbon source
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
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
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
31370	17234 ChEBI	glucose	+	carbon source
31370	29987 ChEBI	glutamate	+	carbon source
31370	17754 ChEBI	glycerol	+	carbon source
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
31370	24996 ChEBI	lactate	+	carbon source
31370	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
31370	15792 ChEBI	malonate	+	carbon source
31370	17306 ChEBI	maltose	+	carbon source
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
31370	29864 ChEBI	mannitol	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
31370	26271 ChEBI	proline	+	carbon source
31370	17272 ChEBI	propionate	+	carbon source
31370	15361 ChEBI	pyruvate	+	carbon source
31370	30031 ChEBI	succinate	+	carbon source
31370	17992 ChEBI	sucrose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

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
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
3837	catalase	+	1.11.1.6
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
3837	cytochrome-c oxidase	+	1.9.3.1
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

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
3837	-	-	-	-	-	+	-	+/-	+	-	+/-	+	-	+	-	-	-	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Condition	#Sulfuric	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3837	sulfidic thermal sea water	New Britain, Matupi Harbour	Papua New Guinea	PNG	Australia and Oceania

Taxonmaps

69479

Global distribution of 16S sequence AY656719 (>99% sequence identity) for Thioclava pacifica from Microbeatlas

Aquatic Samples	159
Soil Samples	63
Animal Samples	75
Plant Samples	7
Total Samples	304

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3837	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	SOAPdenovo v1.05 assembly for Thioclava pacifica DSM 10166	contig	GCA_000714535	1353537.7	2585427686	1353537	71.39

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
3837	Thioclava pacifica strain TL 2 16S ribosomal RNA gene, partial sequence	AY656719	1371		1353537

GC content

3837

GC-content (mol%)63.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: SOAPdenovo v1.05 assembly for Thioclava pacifica DSM 10166
BV-BRC: 1353537.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	88.42	no
125439	motility	BacteriaNetⓘ	yes	52.99	no
125439	gram_stain	BacteriaNetⓘ	negative	91.96	no
125439	spore_formation	BacteriaNetⓘ	no	96.94	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thioclava pacifica DSM 10166
PATRIC: 1353537.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.80	no
125438	anaerobic	anaerobicⓘ	no	84.81	no
125438	spore-forming	spore-formingⓘ	no	91.14	no
125438	aerobic	aerobicⓘ	yes	75.77	yes
125438	thermophilic	thermophileⓘ	no	97.87	yes
125438	flagellated	motile2+ⓘ	yes	72.97	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Interesting Halophilic Sulphur-Oxidising Bacteria with Bioleaching Potential: Implications for Pollutant Mobilisation from Mine Waste.	Opara CB, Kamariah N, Spooren J, Pollmann K, Kutschke S.	Microorganisms	10.3390/microorganisms11010222	2023
Genetics	Osmotic Adaptation and Compatible Solute Biosynthesis of Phototrophic Bacteria as Revealed from Genome Analyses.	Imhoff JF, Rahn T, Kunzel S, Keller A, Neulinger SC.	Microorganisms	10.3390/microorganisms9010046	2020
Metabolism	[Effects of immobilization on community structure and function of sulfide oxidizing microbiota].	Zheng Y, Wang X, Zhao Y, Feng G, Shen Z.	Wei Sheng Wu Xue Bao		2016
Metabolism	Seeking active RubisCOs from the currently uncultured microbial majority colonizing deep-sea hydrothermal vent environments.	Bohnke S, Perner M.	ISME J	10.1038/s41396-019-0439-3	2019
	Biodegradation of thiocyanate by a native groundwater microbial consortium.	Spurr LP, Watts MP, Gan HM, Moreau JW.	PeerJ	10.7717/peerj.6498	2019
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
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
	Thioclava kandeliae sp. nov., Isolated from the Rhizosphere Soil of Mangrove Plant Kandelia candel.	Mou T, Su J, Zhang J, Yu LY, Chen HH, Zhang YQ.	Curr Microbiol	10.1007/s00284-025-04126-z	2025
Phylogeny	Thioclava litoralis sp. nov., a novel species of alphaproteobacterium, isolated from surface seawater.	Chen D, Fan H, Tang S, Gan Z, Lu Y, Long M.	Arch Microbiol	10.1007/s00203-024-04057-6	2024
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
Phylogeny	Tropicimonas isoalkanivorans gen. nov., sp. nov., a branched-alkane-degrading bacterium isolated from Semarang Port in Indonesia.	Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K	Int J Syst Evol Microbiol	10.1099/ijs.0.65822-0	2009
Phylogeny	Thioclava pacifica gen. nov., sp. nov., a novel facultatively autotrophic, marine, sulfur-oxidizing bacterium from a near-shore sulfidic hydrothermal area.	Sorokin DY, Tourova TP, Spiridonova EM, Rainey FA, Muyzer G	Int J Syst Evol Microbiol	10.1099/ijs.0.63415-0	2005

References

#3837	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10166
#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 )
#27683	IJSEM 1069 2005 ( DOI 10.1099/ijs.0.63415-0 , PubMed 15879235 )
#31370	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 #27683
#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) .
#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 .
#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 pacifica (DSM 10166, UNIQEM 229, TL 2)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000714535

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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