Name: Pedobacter alluvionis NWER-II11
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14110

Type strain:

Species: Pedobacter alluvionis

Strain Designation: NWER-II11

Culture col. no.: DSM 19624, LMG 24258

Strain history: <- N. S. Gordon, Univ. Montana, Missoula, USA; NWER-II11

NCBI tax ID(s): 475253 (species)

SI-ID 310963

LMG 24258, DSM 19624, CCM 8562

Section

Pedobacter alluvionis NWER-II11 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from hyporheic sediments.

Gram-negative
rod-shaped
aerobe
psychrophilic
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	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Pedobacter*
	Species	**Pedobacter alluvionis**
	Full Scientific Name (LPSN)	Pedobacter alluvionis Gordon et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28877]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.983

[Ref.: #28877]	Cell length	2 µm

[Ref.: #28877]	Cell width	0.45 µm

[Ref.: #28877]	Cell shape	rod-shaped

[Ref.: #28877]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %91.582

[Ref.: #28877]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8216]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #8216]

Culture medium growth

[Ref.: #8216]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8216]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #8216]	growth	20 °C
[Ref.: #28877]	growth	04-30 °C
[Ref.: #28877]	optimum	17 °C

[Ref.: #8216]	Temperature range	psychrophilic
[Ref.: #28877]	Temperature range	psychrophilic

	pH	Kind of pH		pH
[Ref.: #28877]			optimum	7.5
[Ref.: #28877]			growth	05-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28877]

Oxygen tolerance

aerobe

[Ref.: #28877]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28877]	arabinose ChEBI	+	carbon source
[Ref.: #28877]	cellobiose ChEBI	+	carbon source
[Ref.: #28877]	esculin ChEBI	+	hydrolysis
[Ref.: #28877]	fructose ChEBI	+	carbon source
[Ref.: #28877]	galactose ChEBI	+	carbon source
[Ref.: #28877]	glucose ChEBI	+	carbon source
[Ref.: #28877]	lactose ChEBI	+	carbon source
[Ref.: #28877]	mannose ChEBI	+	carbon source
[Ref.: #28877]	melibiose ChEBI	+	carbon source
[Ref.: #28877]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #28877]	raffinose ChEBI	+	carbon source
[Ref.: #28877]	rhamnose ChEBI	+	carbon source
[Ref.: #28877]	ribitol ChEBI	+	carbon source
[Ref.: #28877]	ribose ChEBI	+	carbon source
[Ref.: #28877]	sucrose ChEBI	+	carbon source
[Ref.: #28877]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #28877]	acid phosphatase	+	3.1.3.2
[Ref.: #28877]	alkaline phosphatase	+	3.1.3.1
[Ref.: #28877]	alpha-galactosidase	+	3.2.1.22
[Ref.: #28877]	catalase	+	1.11.1.6
[Ref.: #28877]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #8216]	Sample type/isolated from	hyporheic sediments
[Ref.: #8216]	Geographic location (country and/or sea, region)	northwestern Montana, Middle Fork Flathead River, Nyack Floodplain
[Ref.: #8216]	Country	USA
[Ref.: #8216]	Country ISO 3 Code	USA
[Ref.: #8216]	Continent	North America
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU030688 (>99% sequence identity) for Pedobacter from Microbeatlas

Aquatic Samples	23
Soil Samples	35
Animal Samples	207
Plant Samples	7
Total Samples	272

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

[Ref.: #8216]

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.: #8216]	Pedobacter alluvionis strain NWER-II11 16S ribosomal RNA gene, partial sequence	EU030688	1400	ENA	475253 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pedobacter alluvionis DSM 19624	GCA_003664035	scaffold	GenBank	475253 tax ID	*
[Ref.: #66792]	Pedobacter alluvionis DSM 19624	GCA_004402005	scaffold	GenBank	475253 tax ID	*
[Ref.: #66792]	Pedobacter alluvionis strain DSM 19624	475253.4	wgs	PATRIC	475253 tax ID	*
[Ref.: #66792]	Pedobacter alluvionis strain DSM 19624	475253.7	wgs	PATRIC	475253 tax ID	*
[Ref.: #66792]	Pedobacter alluvionis DSM 19624	2690315623	draft	JGI IMG/M	475253 tax ID	*

[Ref.: #8216]	GC-content	34.4±0.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #8216]	GC-content	39.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #28877]	GC-content	34.4 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: Pedobacter alluvionis DSM 19624 NCBI: GCA_003664035.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pedobacter alluvionis DSM 19624 NCBI: GCA_003664035.1
[Ref.: #69480]	motile	no	91.787	no
[Ref.: #69480]	flagellated	no	96.879	yes
[Ref.: #69480]	gram-positive	no	97.402	no
[Ref.: #69480]	anaerobic	no	99.586	yes
[Ref.: #69480]	aerobic	yes	85.842	yes
[Ref.: #69480]	halophile	no	95.6	no
[Ref.: #69480]	spore-forming	no	92.494	no
[Ref.: #69480]	glucose-util	yes	91.8	yes
[Ref.: #69480]	thermophile	no	99.426	no
[Ref.: #69480]	glucose-ferment	no	88.709	no

Availability in culture collections External links

[Ref.: #8216]

Culture collection no.

DSM 19624, LMG 24258

[Ref.: #83277]

SI-ID 310963

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pedobacter changchengzhani sp. nov., isolated from soil of Antarctica.	He RH, Liu ZW, Yu Y, Li HR, Du ZJ	Antonie Van Leeuwenhoek	10.1007/s10482-019-01305-4	2019	*
Phylogeny	Pedobacter zeae sp. nov., an endophytic bacterium isolated from maize root.	Gao JL, Sun P, Mao XJ, Du YL, Liu BY, Sun JG	Int J Syst Evol Microbiol	10.1099/ijsem.0.001603	2017	*
Phylogeny	Pedobacter vanadiisoli sp. nov., isolated from soil of a vanadium mine.	Wang Z, Tan Y, Xu D, Wang G, Yuan J, Zheng S	Int J Syst Evol Microbiol	10.1099/ijsem.0.001480	2016	*
Phylogeny	Pedobacterpsychrotolerans sp. nov., isolated from soil.	Manandhar P, Zhang G, Lama A, Hu Y, Gao F	Int J Syst Evol Microbiol	10.1099/ijsem.0.001391	2016	*
Phylogeny	Pedobacter ardleyensis sp. nov., isolated from soil in Antarctica.	Da X, Jiang F, Chang X, Ren L, Qiu X, Kan W, Zhang Y, Deng S, Fang C, Peng F	Int J Syst Evol Microbiol	10.1099/ijsem.0.000504	2015	*
Phylogeny	Pedobacter ureilyticus sp. nov., isolated from tomato rhizosphere soil.	Ngo HTT, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.000055	2015	*
Phylogeny	Pedobacter jejuensis sp. nov., isolated from soil of a pine grove, and emended description of the genus Pedobacter.	Kook M, Park Y, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.058024-0	2014	*
Phylogeny	Pedobacter nyackensis sp. nov., Pedobacter alluvionis sp. nov. and Pedobacter borealis sp. nov., isolated from Montana flood-plain sediment and forest soil.	Gordon NS, Valenzuela A, Adams SM, Ramsey PW, Pollock JL, Holben WE, Gannon JE	Int J Syst Evol Microbiol	10.1099/ijs.0.000158-0	2009	*
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

#8216

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19624

#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 )

#28877

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 #25317 (see below)

#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 )

#83277

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-ID310963.1 )

#25317

IJSEM 1720 2009 ( DOI 10.1099/ijs.0.000158-0 , PubMed 19542109 )

* These data were automatically processed and therefore are not curated

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Pedobacter alluvionis DSM 19624

Pedobacter alluvionis DSM 19624

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