Name: Pacificimonas aurantium DSM 107782
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 157919

Type strain:

Species: Pacificimonas aurantium

Culture col. no.: DSM 107782, CGMCC 1.12399, LMG 27361, JLT 2012

Strain history: <- LMG <- L. Keshao, Xiamen University, College of Oceanography and Environmental Science, China

NCBI tax ID(s): 1250540 (species)

Section

Pacificimonas aurantium DSM 107782 is a mesophilic, Gram-negative bacterium that was isolated from seawater at a depth of 50 m.

Gram-negative
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	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingosinicellaceae*
	Genus	*Pacificimonas*
	Species	"Pacificimonas aurantium"
	Full Scientific Name (LPSN)	Pacificimonas aurantium Li et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.994

Information on culture and growth conditions Culture and growth conditions

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Culture medium

MARINE BROTH (ROTH CP73) (DSMZ Medium 514f)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #64491]			growth	28 °C

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Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.993
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #64491]	24744	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	+

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

[Ref.: #64491]	Sample type/isolated from	seawater at a depth of 50 m
[Ref.: #64491]	Geographic location (country and/or sea, region)	Southeastern Pacific Ocean
[Ref.: #64491]	Country	International waters
[Ref.: #64491]	Geographic location	-3.6833°/-102.5830°
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Marine

What are isolation sources categories?

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Global distribution of 16S sequence JX878395 (>99% sequence identity) for Pacificimonas aurantium subclade from Microbeatlas

Aquatic Samples	650
Soil Samples	51
Animal Samples	71
Plant Samples	2
Total Samples	774

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.: #64491]	Alpha proteobacterium JLT2012 16S ribosomal RNA gene, partial sequence	JX878395	1450	ENA	1250540 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pacificimonas aurantium DSM 107782	GCA_020092905	contig	GenBank	1250540 tax ID	*
[Ref.: #66792]	Pacificimonas aurantium strain DSM 107782	1250540.3	wgs	PATRIC	1250540 tax ID	*

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: Pacificimonas aurantium strain DSM 107782 PATRIC: 1250540.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pacificimonas aurantium strain DSM 107782 PATRIC: 1250540.3
[Ref.: #69480]	motile	yes	69.01	no
[Ref.: #69480]	gram-positive	no	97.669	no
[Ref.: #69480]	anaerobic	no	98.508	no
[Ref.: #69480]	aerobic	yes	90.295	no
[Ref.: #69480]	halophile	no	74.94	no
[Ref.: #69480]	spore-forming	no	94.707	no
[Ref.: #69480]	thermophile	no	97.447	no
[Ref.: #69480]	glucose-util	yes	60.21	yes
[Ref.: #69480]	flagellated	no	85.556	no
[Ref.: #69480]	glucose-ferment	no	94.236	yes

Availability in culture collections External links

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Culture collection no.

DSM 107782, CGMCC 1.12399, LMG 27361, JLT 2012

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Draft Genome Sequence of Pacificimonas aurantium Type Strain JLT2012, Isolated from the Seawater of the Pacific Ocean.	Tang G, Cui R, Tian Y, Lin X	Genome Announc	10.1128/genomeA.00755-17	2017	*
Phylogeny	Pacificimonas aurantium sp. nov., Isolated from the Seawater of the Pacific Ocean.	Li S, Zhou W, Lin D, Tang K, Jiao N	Curr Microbiol	10.1007/s00284-016-0999-7	2016	*

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 )

#64491

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 107782

#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 .

#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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Pacificimonas aurantium strain DSM 107782

Pacificimonas aurantium strain DSM 107782

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