Name: Thiomicrorhabdus chilensis Ch-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11925

Type strain:

Species: Thiomicrorhabdus chilensis

Strain Designation: Ch-1, Chile-1

Culture col. no.: DSM 12352, ATCC 700858

Strain history: <- J. Kuever, Max-Planck-Inst. Marine Microbiology, Bremen, Germany; Chile-1 <- T. Brinkhoff {1997}

NCBI tax ID(s): 1123515 (strain), 63656 (species)

SI-ID 44180

ATCC 700858, DSM 12352

Section

Thiomicrorhabdus chilensis Ch-1 is a chemolithoautotroph, mesophilic, Gram-negative bacterium that was isolated from Thioploca mat.

Gram-negative
motile
rod-shaped
chemolithoautotroph
mesophilic
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Beggiatoales*
	Family	*Piscirickettsiaceae*
	Genus	*Thiomicrorhabdus*
	Species	**Thiomicrorhabdus chilensis**
	Full Scientific Name (LPSN)	Thiomicrorhabdus chilensis (Brinkhoff et al. 1999) Boden et al. 2017

Synonym

Thiomicrospira chilensis

Information on morphological and physiological properties Morphology

[Ref.: #43182]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #43182]	Cell length	0.8-2.0 µm

[Ref.: #43182]	Cell width	0.3-0.5 µm

[Ref.: #43182]	Cell shape	rod-shaped

[Ref.: #43182]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %94.599

[Ref.: #43182]	Flagellum arrangement	monotrichous

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4711]

Culture medium

THIOMICROSPIRA PELOPHILA MEDIUM (DSMZ Medium 142)

[Ref.: #4711]

Culture medium growth

[Ref.: #4711]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4711]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #4711]	growth	25 °C
[Ref.: #43182]	maximum	42 °C
[Ref.: #43182]	minimum	3.5 °C
[Ref.: #43182]	optimum	32-37 °C

[Ref.: #4711]	Temperature range	mesophilic
[Ref.: #43182]	Temperature range	thermophilic
[Ref.: #43182]	Temperature range	psychrophilic
[Ref.: #43182]	Temperature range	mesophilic

		pH
[Ref.: #43182]	maximum	8.5
[Ref.: #43182]	minimum	5.3
[Ref.: #43182]	optimum	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43182]

Nutrition type

chemolithoautotroph

[Ref.: #43182]	Type of spore	endospore
[Ref.: #43182]	Ability of spore formation	no
[Ref.: #43182]	Type of spore	exospore (microbial cyst)
[Ref.: #43182]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Salt		Salt conc.
[Ref.: #43182]	NaCl	optimum	0.47	M
[Ref.: #43182]	NaCl	minimum	0.1	M
[Ref.: #43182]	NaCl	maximum	1.24	M

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43182]	ammonium ChEBI	+	nitrogen source
[Ref.: #43182]	dihydrogen ChEBI	-	electron donor
[Ref.: #43182]	dioxygen ChEBI	+	electron acceptor
[Ref.: #43182]	elemental sulfur ChEBI	+	energy source
[Ref.: #43182]	iron ChEBI	-	electron donor
[Ref.: #43182]	manganese ChEBI	-	electron donor
[Ref.: #43182]	nitrate ChEBI	-	reduction
[Ref.: #43182]	sulfide ChEBI	+	electron donor
[Ref.: #43182]	sulfite ChEBI	-	electron donor
[Ref.: #43182]	tetrathionate ChEBI	+	electron donor
[Ref.: #43182]	thiocyanate ChEBI	-	electron donor
[Ref.: #43182]	thiosulfate ChEBI	+	electron donor
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43182]		cobalamin ChEBI	yes
[Ref.: #43182]		elemental sulfur ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #43182]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43182]	hydrogenase	-	1.12.99.6
[Ref.: #43182]	nitrogenase	-

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

[Ref.: #4711]	Sample type/isolated from	Thioploca mat
[Ref.: #4711]	Host species	Thioploca
[Ref.: #4711]	Geographic location (country and/or sea, region)	Bay of Concepcion
[Ref.: #4711]	Country	Chile
[Ref.: #4711]	Country ISO 3 Code	CHL
[Ref.: #4711]	Continent	Middle and South America

[Ref.: #43182]	Sample type/isolated from	Marine mud
[Ref.: #43182]	Geographic location (country and/or sea, region)	Bay of Conception, Chile
[Ref.: #43182]	Country	Chile
[Ref.: #43182]	Country ISO 3 Code	CHL
[Ref.: #43182]	Continent	Middle and South America
* marker position based on {}

Isolation sources categories

#Environmental	#Microbial community	#Microbial mat
#Host	#Microbial	#Bacteria

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF013975 (>99% sequence identity) for Thiomicrorhabdus chilensis subclade from Microbeatlas

Aquatic Samples	1116
Soil Samples	96
Animal Samples	117
Plant Samples	1
Total Samples	1330

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

[Ref.: #4711]

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.: #4711]	Thiomicrospira sp. Ch-1 16S ribosomal RNA gene, partial sequence	AF013975	1470	ENA	63656 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Thiomicrorhabdus chilensis DSM 12352	GCA_000483485	scaffold	GenBank	1123515 tax ID	*
[Ref.: #66792]	Thiomicrospira chilensis DSM 12352	1123515.3	wgs	PATRIC	1123515 tax ID	*
[Ref.: #66792]	Thiomicrorhabdus chilensis DSM 12352	2537562247	draft	JGI IMG/M	1123515 tax ID	*

[Ref.: #43182]

GC-content

48.1 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Thiomicrorhabdus chilensis DSM 12352 DSM 12352 NCBI: GCA_000483485.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Thiomicrorhabdus chilensis DSM 12352 DSM 12352 NCBI: GCA_000483485.1
[Ref.: #69480]	motile	yes	89.932	yes
[Ref.: #69480]	flagellated	yes	90.288	yes
[Ref.: #69480]	gram-positive	no	98.869	yes
[Ref.: #69480]	anaerobic	no	94.194	no
[Ref.: #69480]	aerobic	no	77.799	no
[Ref.: #69480]	halophile	no	50.702	no
[Ref.: #69480]	spore-forming	no	96.636	no
[Ref.: #69480]	thermophile	no	92.355	no
[Ref.: #69480]	glucose-util	yes	52.335	no
[Ref.: #69480]	glucose-ferment	no	85.081	no

Availability in culture collections External links

[Ref.: #4711]

Culture collection no.

DSM 12352, ATCC 700858

[Ref.: #81139]

SI-ID 44180

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Thiomicrospira chilensis sp. nov., a mesophilic obligately chemolithoautotrophic sulfuroxidizing bacterium isolated from a Thioploca mat.	Brinkhoff T, Muyzer G, Wirsen CO, Kuever J	Int J Syst Bacteriol	10.1099/00207713-49-2-875	1999	*

References

#4711

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12352

#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 )

#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 .

#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 )

#81139

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-ID44180.1 )

* These data were automatically processed and therefore are not curated

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Thiomicrorhabdus chilensis DSM 12352 DSM 12352

Thiomicrorhabdus chilensis DSM 12352 DSM 12352

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