Name: Pseudoxanthomonas kalamensis JA40
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 17509

Type strain:

Species: Pseudoxanthomonas kalamensis

Strain Designation: JA40

Culture col. no.: DSM 18571, ATCC BAA-1031, CIP 108476, CCUG 55486

Strain history: CIP <- 2004, R.M. Harrada, Hawaii Univ., Honolulu, USA: strain ja40

NCBI tax ID(s): 1123030 (strain), 289483 (species)

SI-ID 291133

ATCC BAA-1031, CIP 108476, DSM 18571, CCUG 55486

Special Collections

Section

When using BacDive for research please cite our paper

Pseudoxanthomonas kalamensis JA40 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil and sand contaminated with PAH and PCB.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Pseudoxanthomonas*
	Species	**Pseudoxanthomonas kalamensis**
	Full Scientific Name (LPSN)	Pseudoxanthomonas kalamensis Harada et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #31439]	Gram stain	negative
[Ref.: #120372]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98.994
[Ref.: #125439]	Gram stain	negative Confidence in %98.6

[Ref.: #31439]	Cell length	1-1.25 µm

[Ref.: #31439]	Cell width	0.5 µm

[Ref.: #31439]	Cell shape	rod-shaped
[Ref.: #120372]	Cell shape	rod-shaped

[Ref.: #31439]	Motility	no
[Ref.: #120372]	Motility	no

[Ref.: #60604]

Incubation period

2 days

[Ref.: #31439]	Pigment production	yes
[Ref.: #120372]	Pigment production	no
[Ref.: #120372]	Pigment name	Pyocyanin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7531]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #7531]

Culture medium growth

[Ref.: #7531]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7531]

Culture medium composition

expand / minimize

[Ref.: #33244]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #33244]

Culture medium growth

[Ref.: #33244]

Culture medium composition

expand / minimize

[Ref.: #120372]

Culture medium

CIP Medium 72

[Ref.: #120372]

Culture medium growth

[Ref.: #120372]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #7531]		growth	30 °C
[Ref.: #31439]		growth	28-37 °C
[Ref.: #31439]		optimum	30-37 °C
[Ref.: #33244]		growth	30 °C
[Ref.: #60604]		growth	30-37 °C
[Ref.: #120372]		growth	25-37 °C
[Ref.: #120372]	negative	growth	10 °C
[Ref.: #120372]	negative	growth	41 °C

	pH	Kind of pH		pH
[Ref.: #31439]			optimum	7
[Ref.: #31439]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31439]	Oxygen tolerance	aerobe
[Ref.: #60604]	Oxygen tolerance	aerobe
[Ref.: #120372]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	aerobe Confidence in %93.4

[Ref.: #31439]	Ability of spore formation	no
[Ref.: #125438]	Ability of spore formation	no Confidence in %94.312
[Ref.: #125439]	Ability of spore formation	no Confidence in %98.7

	Salt	Tested relation		Salt conc.
[Ref.: #31439]	NaCl		growth	0.5-3	%
[Ref.: #31439]	NaCl		optimum	2	%
[Ref.: #120372]	NaCl		growth	0-4	%
[Ref.: #120372]	NaCl	no	growth	6	%
[Ref.: #120372]	NaCl	no	growth	8	%
[Ref.: #120372]	NaCl	no	growth	10	%

[Ref.: #31439]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31439]	alanine ChEBI	+	carbon source
[Ref.: #31439]	alpha-cyclodextrin ChEBI	+	carbon source
[Ref.: #31439]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #31439]	cellobiose ChEBI	+	carbon source
[Ref.: #120372]	citrate ChEBI	-	carbon source
[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.: #31439]	dextrin ChEBI	+	carbon source
[Ref.: #31439]	esculin ChEBI	+	hydrolysis
[Ref.: #120372]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #31439]	fructose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31439]	glucose ChEBI	+	carbon source
[Ref.: #31439]	glutamate ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #31439]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #31439]	mannose ChEBI	+	carbon source
[Ref.: #31439]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #120372]	nitrate ChEBI	-	reduction
[Ref.: #120372]	nitrate ChEBI	-	respiration
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #120372]	nitrite ChEBI	-	reduction
[Ref.: #31439]	raffinose ChEBI	+	carbon source
[Ref.: #31439]	salicin ChEBI	+	carbon source
[Ref.: #31439]	serine ChEBI	+	carbon source
[Ref.: #31439]	sucrose ChEBI	+	carbon source
[Ref.: #31439]	trehalose ChEBI	+	carbon source
[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.

	Antibiotica	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #120372]		0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)	no	yes

	Metabolite production	Metabolite	Production
[Ref.: #120372]		indole ChEBI	no
[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.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #120372]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #120372]	amylase	-
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #120372]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym, API 20NE
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #120372]	caseinase	-	3.4.21.50
[Ref.: #31439]	catalase	+	1.11.1.6
[Ref.: #120372]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31439]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #120372]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #120372]	gelatinase	-
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #120372]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #120372]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #120372]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120372]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120372]	oxidase	+
[Ref.: #120372]	protease	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #120372]	tryptophan deaminase	-
[Ref.: #120372]	tween esterase	-
[Ref.: #120372]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #7531]	25920	-	-	-	-	-	+	-	+	+	-	-	-	+	+	-	-	-	-	-	-	+

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #120372]	11213	-	+	+	+	-	+	+	-	+	-	+	+	-	-	-	+	+	+	-	-

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

[Ref.: #7531]	Sample type/isolated from	soil and sand contaminated with PAH and PCB
[Ref.: #7531]	Geographic location (country and/or sea, region)	Pacific Ocean, Johnston Atoll
[Ref.: #7531]	Country	USA
[Ref.: #7531]	Country ISO 3 Code	USA
[Ref.: #7531]	Continent	North America
[Ref.: #7531]	Geographic location	16.7333°/-169.5330°

[Ref.: #60604]	Sample type/isolated from	Soil contaminated with PCB's+PAH's
[Ref.: #60604]	Sampling date	2003
[Ref.: #60604]	Geographic location (country and/or sea, region)	Kalama Island,Johnston Atoll

[Ref.: #120372]	Sample type/isolated from	Environment, Soil contaminated with PCB's + PAH's
[Ref.: #120372]	Geographic location (country and/or sea, region)	Johnston atoll, Kalama Island
[Ref.: #120372]	Country	United States of America
[Ref.: #120372]	Country ISO 3 Code	USA
[Ref.: #120372]	Continent	North America
[Ref.: #120372]	Isolation date	2003
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Environmental	#Terrestrial	#Sandy
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY686710 (>99% sequence identity) for Xanthomonas from Microbeatlas

Aquatic Samples	31
Soil Samples	17
Animal Samples	14
Plant Samples	26
Total Samples	88

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

[Ref.: #7531]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120372]	Biosafety level	1	Risk group (French classification)

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.: #7531]	Pseudoxanthomonas kalamensis strain JA40 16S ribosomal RNA gene, partial sequence	AY686710	1457	GenBank ENA	289483 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pseudoxanthomonas kalamensis DSM 18571	GCA_010211745	contig	GenBank ENA	1123030 tax ID	*
[Ref.: #66792]	Pseudoxanthomonas kalamensis DSM 18571	1123030.3	wgs	PATRIC	1123030 tax ID	*
[Ref.: #66792]	Pseudoxanthomonas kalamensis DSM 18571	2571042364	draft	JGI IMG/M	1123030 tax ID	*

[Ref.: #31439]

GC-content

64 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudoxanthomonas kalamensis DSM 18571 PATRIC: 1123030.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.994	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	95.103	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	94.312	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	84.331	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	94.873	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	75.544	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudoxanthomonas kalamensis DSM 18571 NCBI: GCA_010211745
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	87.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	98.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	93.4

Availability in culture collections External links

[Ref.: #7531]

Culture collection no.

DSM 18571, ATCC BAA-1031, CIP 108476, CCUG 55486

[Ref.: #86506]

SI-ID 291133

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudoxanthomonas helianthi sp. nov., isolated from roots of Jerusalem artichoke (Helianthus tuberosus).	Kittiwongwattana C, Thawai C	Int J Syst Evol Microbiol	10.1099/ijsem.0.001465	2016	*
Phylogeny	Pseudoxanthomonas kalamensis sp. nov., a novel gammaproteobacterium isolated from Johnston Atoll, North Pacific Ocean.	Harada RM, Campbell S, Li QX	Int J Syst Evol Microbiol	10.1099/ijs.0.63556-0	2006	*

References

#7531

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18571

#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 )

#31439

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 #27744 (see below)

#33244 ; Curators of the CIP;
#60604 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55486

#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 .

#68382

Automatically annotated from API zym .

#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 .

#86506

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-ID291133.1 )

#120372 Collection of Institut Pasteur ; Curators of the CIP; CIP 108476

#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 .

#27744

IJSEM 1103 2006 ( DOI 10.1099/ijs.0.63556-0 , PubMed 16627662 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Pseudoxanthomonas kalamensis in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Pseudoxanthomonas kalamensis DSM 18571

Pseudoxanthomonas kalamensis DSM 18571

Change proposal

Change proposal