Thiomicrorhabdus arctica (DSM 13458, ATCC 700955, SVAL-E)

Name: Thiomicrorhabdus arctica (DSM 13458, ATCC 700955, SVAL-E)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11931

Type strain

Strain Designation SVAL-E

Culture col. no. DSM 13458 ATCC 700955 SVAL-E

NCBI tax ID(s) 1123514 131540

Special Collections DSMZ Literature strains

History <- K. Ravenschlag, Max-Planck-Inst. Marine Microbiology, Bremen, Germany; SVAL-E <- K. Ravenschlag; {1998}

Links

Thiomicrorhabdus arctica SVAL-E is an aerobe, chemolithoautotroph, Gram-negative bacterium that was isolated from marine Arctic sediments.

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

Name and taxonomic classification

SI-ID 118511

ATCC 700955,DSM 13458

@ref 20215

Last LPSN update 2026-02-09 11:20:42

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Beggiatoales

Family Piscirickettsiaceae

Genus Thiomicrorhabdus

Species Thiomicrorhabdus arctica

Full scientific name Thiomicrorhabdus arctica (Knittel et al. 2005) Boden et al. 2017

Synonyms (1)

Thiomicrospira arctica

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Flagellum arrangement	Confidence
31345	negative	1.35 µm	0.55 µm	rod-shaped
43182	negative	1.2-1.5 µm	0.5-0.6 µm	rod-shaped	monotrichous
125438	negative					99.5
125439	negative					99.1

Colony morphology

5050

Incubation period8-14 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5050	THIOMICRORHABDUS MEDIUM (DSMZ Medium 142a)		Medium recipe at MediaDive	Name: THIOMICRORHABDUS MEDIUM (DSMZ Medium 142a) Composition: NaCl 15.0 g/l Na2S2O3 x 5 H2O 5.0 g/l MgSO4 x 7 H2O 1.5 g/l (NH4)2SO4 1.0 g/l K2HPO4 0.5 g/l CaCl2 x 2 H2O 0.42 g/l Bromothymol blue 0.004 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Pyridoxine hydrochloride 0.0003 g/l Nicotinic acid 0.0002 g/l Thiamine-HCl x 2 H2O 0.0002 g/l CoCl2 x 6 H2O 0.00019 g/l Calcium pantothenate 0.0001 g/l MnCl2 x 4 H2O 0.0001 g/l Vitamin B12 0.0001 g/l p-Aminobenzoic acid 8e-05 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l D-(+)-biotin 2e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
5050	positive	growth	15
31345	positive	optimum	12.35
43182	positive	maximum	20.8
43182	positive	minimum	-2
43182	positive	optimum	11.5-13.2

Culture pH

@ref	Ability	Type	PH	PH range
43182	positive	maximum	9
43182	positive	minimum	6.5
31345	positive	optimum	7.75
43182	positive	optimum	7.3-8.0
31345	positive	growth	6.5-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31345	aerobe
125439	obligate aerobe	98.9

Nutrition type

43182

Typechemolithoautotroph

Spore formation

@ref	Type of spore	Confidence
31345
43182	endospore
43182	exospore (microbial cyst)
125438		92.217
125439		99

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31345	NaCl	positive	optimum	1.45 %
43182	NaCl	positive	optimum	0.25 M
43182	NaCl	positive	minimum	0.04 M
43182	NaCl	positive	maximum	1.24 M

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43182	28938 ChEBI	ammonium	+	nitrogen source
43182	18276 ChEBI	dihydrogen	-	electron donor
43182	15379 ChEBI	dioxygen	+	electron acceptor
43182	18248 ChEBI	iron	-	electron donor
43182	18291 ChEBI	manganese	-	electron donor
43182	17632 ChEBI	nitrate	-	reduction
43182	15138 ChEBI	sulfide	+	electron donor
43182	17359 ChEBI	sulfite	-	electron donor
43182	15226 ChEBI	tetrathionate	+	electron donor
43182	18022 ChEBI	thiocyanate	-	electron donor
43182	16094 ChEBI	thiosulfate	+	electron donor

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43182	30411 ChEBI	cobalamin
43182	33403 ChEBI	elemental sulfur

Enzymes

@ref	Value	Activity	Ec
43182	cytochrome oxidase	+	1.9.3.1
43182	hydrogenase	-	1.12.99.6
43182	nitrogenase	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Condition	#Psychrophilic (<10°C)	-
#Climate	#Cold	#Polar

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5050	marine Arctic sediments	coast of Svalbard	Norway	NOR	Europe
43182	Marine sediment, Svalbard	northern, arctic, Svalbard	Norway	NOR	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ404731 (>99% sequence identity) for Thiomicrorhabdus from Microbeatlas

Aquatic Samples	105
Soil Samples	5
Animal Samples	22
Plant Samples
Total Samples	132

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5050	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	ASM38108v1 assembly for Thiomicrorhabdus arctica DSM 13458	scaffold	GCA_000381085	1123514.3	2522572127	1123514	78.08

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5050	Thiomicrospira arctica 16S rRNA gene	AJ404731	1426		131540

GC content

@ref	GC-content (mol%)
5050	42.4
43182	41.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Thiomicrorhabdus arctica DSM 13458
NCBI: GCA_000381085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.00	no
125439	motility	BacteriaNetⓘ	yes	73.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thiomicrorhabdus arctica DSM 13458 DSM 13458
NCBI: GCA_000381085.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	yes
125438	anaerobic	anaerobicⓘ	no	87.87	yes
125438	aerobic	aerobicⓘ	yes	56.29	no
125438	spore-forming	spore-formingⓘ	no	92.22	no
125438	thermophilic	thermophileⓘ	no	92.44	no
125438	flagellated	motile2+ⓘ	yes	73.73	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Diversity in CO₂-Concentrating Mechanisms among Chemolithoautotrophs from the Genera Hydrogenovibrio, Thiomicrorhabdus, and Thiomicrospira, Ubiquitous in Sulfidic Habitats Worldwide.	Scott KM, Leonard JM, Boden R, Chaput D, Dennison C, Haller E, Harmer TL, Anderson A, Arnold T, Budenstein S, Brown R, Brand J, Byers J, Calarco J, Campbell T, Carter E, Chase M, Cole M, Dwyer D, Grasham J, Hanni C, Hazle A, Johnson C, Johnson R, Kirby B, Lewis K, Neumann B, Nguyen T, Nino Charari J, Morakinyo O, Olsson B, Roundtree S, Skjerve E, Ubaldini A, Whittaker R.	Appl Environ Microbiol	10.1128/aem.02096-18	2019
Phylogeny	Thiomicrospira arctica sp. nov. and Thiomicrospira psychrophila sp. nov., psychrophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacteria isolated from marine Arctic sediments.	Knittel K, Kuever J, Meyerdierks A, Meinke R, Amann R, Brinkhoff T	Int J Syst Evol Microbiol	10.1099/ijs.0.63362-0	2005

References

#5050	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13458
#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 )
#27659	IJSEM 781 2005 ( DOI 10.1099/ijs.0.63362-0 , PubMed 15774662 )
#31345	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 #27659
#43182	Rich Boden, Kathleen M. Scott, John Williams, Sydney Russel, Kirsten Antonen, Alex W. Rae and Lee P. Hutt: An evaluation of Thiomicrospira, Hydrogenovibrio and Thioalkalimicrobium: reclassification of four species of Thiomicrospira to each Thiomicrorhabdus gen. nov. and Hydrogenovibrio, and reclassification of all four species of Thioalkalimicrobium to Thiomicrospira. IJSEM 67: 1140 - 1151 2017 ( DOI 10.1099/ijsem.0.001855 , PubMed 28581925 )
#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) .
#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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Thiomicrorhabdus arctica (DSM 13458, ATCC 700955, SVAL-E)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000381085

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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