Name: Ciceribacter thiooxidans F43b
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158569

Type strain:

Species: Ciceribacter thiooxidans

Strain Designation: F43b

Culture col. no.: CCTCC AB 2016062, KCTC 52231

Strain history: <- Tongchu Deng, Guangdong Institute of Microbiology.

NCBI tax ID(s): 1969821 (species)

Section

Ciceribacter thiooxidans F43b is a facultative anaerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from From sediment, electronic waste pollution..

colony-forming
Gram-negative
motile
rod-shaped
facultative anaerobe
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	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Rhizobiaceae*
	Genus	*Ciceribacter*
	Species	**Ciceribacter thiooxidans**
	Full Scientific Name (LPSN)	Ciceribacter thiooxidans Deng et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #65591]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.986

[Ref.: #65591]	Cell length	1-2 µm

[Ref.: #65591]	Cell width	0.6-0.8 µm

[Ref.: #65591]	Cell shape	rod-shaped

[Ref.: #65591]	Motility	yes

[Ref.: #65591]	Colony size	10 mm
[Ref.: #65591]	Colony shape	circular
[Ref.: #65591]	Cultivation medium used	DSMZ medium 98 agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65591]

Culture medium

DSMZ medium 98 agar

[Ref.: #65591]

Culture medium growth

[Ref.: #65591]

Culture medium

LB (Luria-Bertani) MEDIUM

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Culture medium growth

		Temperature
[Ref.: #65591]	growth	20-42 °C
[Ref.: #65591]	optimum	37 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #65591]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65591]			optimum	7.5
[Ref.: #65591]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65591]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #65591]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.982
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65591]		NaCl		growth	0-3.5	%(w/v)

[Ref.: #65591]

Observation

facultatively chemolithotrophic

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65591]	4-hydroxyphenylacetic acid ChEBI	-	carbon source
[Ref.: #65591]	acetate ChEBI	+	carbon source
[Ref.: #65591]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #65591]	D-arabitol ChEBI	+	carbon source
[Ref.: #65591]	D-fructose ChEBI	+	carbon source
[Ref.: #65591]	D-galactose ChEBI	+	carbon source
[Ref.: #65591]	D-mannitol ChEBI	+	carbon source
[Ref.: #65591]	D-mannose ChEBI	+	carbon source
[Ref.: #65591]	D-sorbitol ChEBI	+	carbon source
[Ref.: #65591]	formate ChEBI	+	carbon source
[Ref.: #65591]	fucose ChEBI	+	carbon source
[Ref.: #65591]	glycine-proline ChEBI	-	carbon source
[Ref.: #65591]	hydrogencarbonate ChEBI	+	carbon source
[Ref.: #65591]	L-alanine ChEBI	+	carbon source
[Ref.: #65591]	L-arginine ChEBI	+	carbon source
[Ref.: #65591]	L-histidine ChEBI	-	carbon source
[Ref.: #65591]	N-acetyl-beta-D-mannosamine ChEBI	-	carbon source
[Ref.: #65591]	N-acetylgalactosamine ChEBI	-	carbon source
[Ref.: #65591]	nitrate ChEBI	+	reduction
[Ref.: #65591]	propionate ChEBI	+	carbon source
[Ref.: #65591]	sucrose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #67771]	Sample type/isolated from	From sediment, electronic waste pollution.
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia

[Ref.: #65591]	Sample type/isolated from	sediment sample of sulfide-rich anoxic sediment
[Ref.: #65591]	Geographic location (country and/or sea, region)	urban creek in the Pearl River Delta
[Ref.: #65591]	Country	China
[Ref.: #65591]	Country ISO 3 Code	CHN
[Ref.: #65591]	Continent	Asia
[Ref.: #65591]	Enrichment culture duration	2 weeks
[Ref.: #65591]	Isolation/enrichment procedure	sample (10 g) was added to the enrichment medium (100 ml), which was incubated for 2 weeks and sub-cultured three times. After serial dilution with distilled water, 0.1 ml culture suspension was spread onto agar plates. The plates were incubated at 30°C in an anaerobic chamber.
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Condition	#Anoxic (anaerobic)	-
#Condition	#Sulfuric	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU975391 (>99% sequence identity) for Rhizobiaceae from Microbeatlas

Aquatic Samples	199
Soil Samples	369
Animal Samples	56
Plant Samples	29
Total Samples	653

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.: #65591]	16S rRNA gene sequence	KU975391		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ciceribacter thiooxidans F43B	GCA_014126615	complete	GenBank	1969821 tax ID	*

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GC-content

66 mol%

genome sequence analysis

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: Ciceribacter thiooxidans F43B NCBI: GCA_014126615.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ciceribacter thiooxidans F43B NCBI: GCA_014126615.1
[Ref.: #69480]	flagellated	no	68.861	no
[Ref.: #69480]	gram-positive	no	98.436	yes
[Ref.: #69480]	anaerobic	no	97.338	yes
[Ref.: #69480]	aerobic	yes	89.008	no
[Ref.: #69480]	halophile	no	81.268	no
[Ref.: #69480]	spore-forming	no	96.497	no
[Ref.: #69480]	thermophile	no	96.42	no
[Ref.: #69480]	glucose-util	yes	91.56	yes
[Ref.: #69480]	motile	yes	91.236	yes
[Ref.: #69480]	glucose-ferment	no	90.681	no

Availability in culture collections External links

[Ref.: #65591]

Culture collection no.

CCTCC AB 2016062, KCTC 52231

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium flavescens sp. nov., Isolated from a Chlorothalonil-Contaminated Soil.	Su XJ, Liu GP, Zhang L, Zhou XY, Qiao WJ, Jiang JD	Curr Microbiol	10.1007/s00284-021-02462-4	2021	*
Phylogeny	Ciceribacter thiooxidans sp. nov., a novel nitrate-reducing thiosulfate-oxidizing bacterium isolated from sulfide-rich anoxic sediment.	Deng T, Chen X, Zhang Q, Zhong Y, Guo J, Sun G, Xu M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002367	2017	*

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 )

#65591

Tongchu Deng, Xingjuan Chen, Qin Zhang, Yuming Zhong, Jun Guo, Guoping Sur, Meiying Xu: Ciceribacter thiooxidans sp. nov., a novel nitrate-reducing thiosulfate-oxidizing bacterium isolated from sulfide-rich anoxic sediment. IJSEM 67: 4710 - 4715 2017 ( DOI 10.1099/ijsem.0.002367 , PubMed 28984561 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

* These data were automatically processed and therefore are not curated

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Ciceribacter thiooxidans F43B

Ciceribacter thiooxidans F43B

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