Name: Pedobacter jamesrossensis LMG 29684
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133113

Type strain:

Species: Pedobacter jamesrossensis

Culture col. no.: LMG 29684, CCM 8689

NCBI tax ID(s): 1908238 (species)

Section

Pedobacter jamesrossensis LMG 29684 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from stone fragments.

colony-forming
Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Pedobacter*
	Species	**Pedobacter jamesrossensis**
	Full Scientific Name (LPSN)	Pedobacter jamesrossensis Švec et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25302]	Gram stain	negative
[Ref.: #25302]	Cell length	1.0-1.2 µm
[Ref.: #25302]	Cell width	0.5 µm
[Ref.: #25302]	Cell shape	rod-shaped
[Ref.: #25302]	Motility	no

[Ref.: #25302]	Gram stain	negative
[Ref.: #25302]	Cell length	0.9-1.4 µm
[Ref.: #25302]	Cell width	0.4-0.5 µm
[Ref.: #25302]	Cell shape	rod-shaped
[Ref.: #25302]	Motility	no

[Ref.: #25302]	Gram stain	negative
[Ref.: #25302]	Cell length	1.0-1.3 µm
[Ref.: #25302]	Cell width	0.5 µm
[Ref.: #25302]	Cell shape	rod-shaped
[Ref.: #25302]	Motility	no

[Ref.: #25302]	Gram stain	negative
[Ref.: #25302]	Cell length	1.2-1.6 µm
[Ref.: #25302]	Cell width	0.6 µm
[Ref.: #25302]	Cell shape	rod-shaped
[Ref.: #25302]	Motility	no

[Ref.: #25302]	Colony size	1-2 mm
[Ref.: #25302]	Colony color	reddish
[Ref.: #25302]	Colony shape	circular
[Ref.: #25302]	Incubation period	5 days
[Ref.: #25302]	Cultivation medium used	R2A agar

[Ref.: #25302]	Colony size	1-2 mm
[Ref.: #25302]	Colony color	reddish
[Ref.: #25302]	Colony shape	circular
[Ref.: #25302]	Incubation period	5 days
[Ref.: #25302]	Cultivation medium used	R2A

[Ref.: #25302]	Colony size	1-2 mm
[Ref.: #25302]	Colony color	pink
[Ref.: #25302]	Colony shape	circular
[Ref.: #25302]	Incubation period	5 days
[Ref.: #25302]	Cultivation medium used	R2A

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

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Culture medium

nutritient agar

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Culture medium growth

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Culture medium

tryptone soy agar (TSA)

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Culture medium growth

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Culture medium

brain heart infusion agar

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Culture medium growth

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Culture medium

nutritient agar (NA)

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Culture medium growth

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Culture medium

MacConkey agar

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Culture medium growth

	Kind of temperature		Temperature
[Ref.: #25302]		growth	1-30 °C
[Ref.: #25302]	no	growth	35 °C
[Ref.: #25302]		optimum	20 °C

[Ref.: #25302]	Temperature range	mesophilic
[Ref.: #25302]	Temperature range	psychrophilic

	Kind of pH		pH
[Ref.: #25302]		optimum	8
[Ref.: #25302]		growth	6-10
[Ref.: #25302]		growth	6-8
[Ref.: #25302]	inconsistent	growth	9
[Ref.: #25302]	no	growth	10
[Ref.: #25302]		growth	6-9
[Ref.: #25302]	inconsistent	growth	10
[Ref.: #25302]	no	growth	5
[Ref.: #25302]	no	growth	11

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

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Ability of spore formation

	Salt	Tested relation		Salt conc.
[Ref.: #25302]	NaCl		growth	0-1	%(w/v)
[Ref.: #25302]	NaCl	no	growth	2	%(w/v)
[Ref.: #25302]	NaCl		growth	0-2	%(w/v)
[Ref.: #25302]	NaCl		growth	1-2	%(w/v)
[Ref.: #25302]	NaCl	no	growth	3	%(w/v)
[Ref.: #25302]	NaCl		optimum	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25302]	acetamide ChEBI	-	growth
[Ref.: #25302]	casein	-	hydrolysis
[Ref.: #25302]	casein	+	hydrolysis
[Ref.: #25302]	citrate ChEBI	-	carbon source
[Ref.: #25302]	dna ChEBI	-	hydrolysis
[Ref.: #25302]	dna ChEBI	+	hydrolysis
[Ref.: #25302]	esculin ChEBI	+	hydrolysis
[Ref.: #25302]	esculin ChEBI	+/-	hydrolysis
[Ref.: #25302]	gelatin ChEBI	-	hydrolysis
[Ref.: #25302]	gelatin ChEBI	+	hydrolysis
[Ref.: #25302]	lecithin ChEBI	-	hydrolysis
[Ref.: #25302]	nitrate ChEBI	-	reduction
[Ref.: #25302]	nitrite ChEBI	-	reduction
[Ref.: #25302]	sodium malonate ChEBI	-	growth
[Ref.: #25302]	starch ChEBI	-	hydrolysis
[Ref.: #25302]	starch ChEBI	+	hydrolysis
[Ref.: #25302]	tween 80 ChEBI	-	hydrolysis
[Ref.: #25302]	tween 80 ChEBI	+	hydrolysis
[Ref.: #25302]	tween 80 ChEBI	+/-	hydrolysis
[Ref.: #25302]	tyrosine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25302]		indole ChEBI	no

	Physiological tests	Metabolite	Citrate test
[Ref.: #25302]		citrate ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25302]	acid phosphatase	+	3.1.3.2
[Ref.: #25302]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25302]	alpha-fucosidase	+/-	3.2.1.51
[Ref.: #25302]	alpha-fucosidase	+	3.2.1.51
[Ref.: #25302]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25302]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25302]	alpha-galactosidase	+	3.2.1.22
[Ref.: #25302]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25302]	alpha-mannosidase	+	3.2.1.24
[Ref.: #25302]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25302]	beta-galactosidase	+	3.2.1.23
[Ref.: #25302]	beta-glucosidase	+	3.2.1.21
[Ref.: #25302]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25302]	catalase	+	1.11.1.6
[Ref.: #25302]	chymotrypsin	-	3.4.4.5
[Ref.: #25302]	cystine arylamidase	+/-	3.4.11.3
[Ref.: #25302]	cystine arylamidase	+	3.4.11.3
[Ref.: #25302]	cystine arylamidase	-	3.4.11.3
[Ref.: #25302]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25302]	esterase (C 4)	+/-
[Ref.: #25302]	esterase (C 4)	-
[Ref.: #25302]	esterase Lipase (C 8)	+
[Ref.: #25302]	leucine arylamidase	+	3.4.11.1
[Ref.: #25302]	lipase (C 14)	-
[Ref.: #25302]	lysine decarboxylase	-	4.1.1.18
[Ref.: #25302]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #25302]	naphthol-AS-BI-phosphohydrolase	+/-
[Ref.: #25302]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25302]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #25302]	trypsin	+	3.4.21.4
[Ref.: #25302]	urease	-	3.5.1.5
[Ref.: #25302]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25302]

Fatty acid	Percentage
C16:1ω7c / C16:1ω6c	34.7
C15:0 iso	12
C17:0 iso 3OH	11.4
C15:0 anteiso	7.6
C16:0 iso 3OH	6.6
C17:0 2OH	6.6
C16:1ω5c	4
C16:0 10-methyl / iso-C17:1ω9c	2.9
C16:0 3OH	1.9
C16:0 iso	1.8
C11:0 anteiso	1.5
C15:0 iso 3OH	1.4
C17:1 anteiso ω9c	1.3
C16:1 iso H	1.2
C15:0 2OH	1.1

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

[Ref.: #25302]	Sample type/isolated from	stone fragments
[Ref.: #25302]	Geographic location (country and/or sea, region)	Devils Rocks, James Ross Island
[Ref.: #25302]	Country	Antarctica
[Ref.: #25302]	Country ISO 3 Code	ATA
[Ref.: #25302]	Continent	Australia and Oceania
[Ref.: #25302]	Geographic location	-63.0000°/-57.0000°
[Ref.: #25302]	Enrichment culture	R2A agar
[Ref.: #25302]	Enrichment culture duration	5-7 days
[Ref.: #25302]	Enrichment culture temperature	15 ̊C
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

What are isolation sources categories?

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.: #25302]	Pedobacter sp. RP02016a strain CCM 8689 16S ribosomal RNA gene, partial sequence	KX611467	1474	GenBank	1908238 tax ID
[Ref.: #25302]	Pedobacter sp. RP02016b strain CCM 8691 16S ribosomal RNA gene, partial sequence	KX611475	1483	GenBank	1908239 tax ID
[Ref.: #25302]	Pedobacter sp. RP02016c strain CCM 8685 16S ribosomal RNA gene, partial sequence	KX611477	1474	GenBank	1908240 tax ID
[Ref.: #25302]	Pedobacter sp. RP02016d strain CCM 8687 16S ribosomal RNA gene, partial sequence	KX611481	1472	GenBank	1908241 tax ID

[Ref.: #25302]	GC-content	36.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #25302]	GC-content	35.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #25302]	GC-content	35.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #25302]	GC-content	38.8 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #25302]

Culture collection no.

LMG 29684, CCM 8689

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter jamesrossensis sp. nov., Pedobacter lithocola sp. nov., Pedobacter mendelii sp. nov. and Pedobacter petrophilus sp. nov., isolated from the Antarctic environment.	Svec P, Kralova S, Busse HJ, Kleinhagauer T, Pantucek R, Maslanova I, Cnockaert M, Vandamme P, Stankova E, Gelbicova T, Holochova P, Bartak M, Kyrova K, Sedlacek I	Int J Syst Evol Microbiol	10.1099/ijsem.0.001749	2017	*
Phylogeny	Pedobacter mucosus sp. nov., isolated from a soil sample of glacier foreland in Austre Lovenbreen, Arctic.	Huang J, Peng X, Qin K, Liu Y, Niu J, Liu J, Dong J, Zhang Y, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.005448	2022	*

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 )

#25302

P. K. Svec, S.,Busse, H. J.,Kleinhagauer, T.,Pantucek, R.,Maslanová, I.,Cnockaert, M.,Vandamme, P.,Stanková, E.,Gelbícová, T.,Holochová, Pavla,Barták, M.,Kýrová, Kamila,Sedlácek, I.: Pedobacter jamesrossensis sp. nov., Pedobacter lithocola sp. nov., Pedobacter mendelii sp. nov. and Pedobacter petrophilus sp. nov., isolated from the Antarctic environment. IJSEM 67: 1499 - 1507 2017 ( DOI 10.1099/ijsem.0.001749 , PubMed 27995868 )

* These data were automatically processed and therefore are not curated

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