Name: Edaphobacter lichenicola DSM 104462
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158304

Type strain:

Species: Edaphobacter lichenicola

Culture col. no.: DSM 104462, SBC 68, VKM B-3208

Strain history: <- S. Dedysh; Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Moscow, RUSSIA; SBC68<-S. E. Belova

NCBI tax ID(s): 2051959 (species)

SI-ID 397404

DSM 104462

Special Collections

Section

Edaphobacter lichenicola DSM 104462 is an obligate aerobe, Gram-negative, rod-shaped bacterium that was isolated from Lichen thalli collected from forested tundra.

Gram-negative
rod-shaped
obligate aerobe
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	*Acidobacteriota*
	Class	*Terriglobia*
	Order	*Terriglobales*
	Family	*Acidobacteriaceae*
	Genus	*Edaphobacter*
	Species	**Edaphobacter lichenicola**
	Full Scientific Name (LPSN)	Edaphobacter lichenicola Belova et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66552]	Gram stain	negative

[Ref.: #66552]	Cell length	1.3-2.7 µm

[Ref.: #66552]	Cell width	0.4-0.7 µm

[Ref.: #66552]	Cell shape	rod-shaped

[Ref.: #66552]	Motility	no

[Ref.: #66552]

Colony color

light pink

Information on culture and growth conditions Culture and growth conditions

[Ref.: #64965]

Culture medium

GRANULICELLA MEDIUM (DSMZ Medium 1284)

[Ref.: #64965]

Culture medium growth

[Ref.: #64965]

Culture medium link

Medium recipe at MediaDive

[Ref.: #64965]

Culture medium composition

expand / minimize

[Ref.: #66552]

Culture medium

[Ref.: #66552]

Culture medium growth

		Temperature
[Ref.: #64965]	growth	25 °C
[Ref.: #66552]	optimum	20-30 °C
[Ref.: #66552]	growth	7-37 °C

	pH	Kind of pH		pH
[Ref.: #66552]			optimum	4.3-5.6
[Ref.: #66552]			growth	3.4-7.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66552]

Oxygen tolerance

obligate aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66552]		NaCl		growth	0-1	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66552]	acetic acid ChEBI	-	assimilation
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #66552]	arabinogalactan ChEBI	+	hydrolysis
[Ref.: #66552]	arbutin ChEBI	+/-	growth
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #66552]	butyrate ChEBI	-	assimilation
[Ref.: #66552]	cellobiose ChEBI	+	carbon source
[Ref.: #66552]	cellulose ChEBI	-	hydrolysis
[Ref.: #66552]	chitin ChEBI	-	hydrolysis
[Ref.: #66552]	chitosan ChEBI	-	hydrolysis
[Ref.: #66552]	citric acid ChEBI	-	assimilation
[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.: #66552]	dextrin ChEBI	+	hydrolysis
[Ref.: #66552]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #66552]	ethanol ChEBI	+	carbon source
[Ref.: #66552]	formate ChEBI	-	assimilation
[Ref.: #66552]	fructose ChEBI	+	carbon source
[Ref.: #66552]	fucoidan ChEBI	-	hydrolysis
[Ref.: #66552]	fucose ChEBI	+/-	growth
[Ref.: #66552]	fumarate ChEBI	+/-	growth
[Ref.: #66552]	galactitol ChEBI	-	assimilation
[Ref.: #66552]	galactomannan ChEBI	+	hydrolysis
[Ref.: #66552]	galactose ChEBI	+	carbon source
[Ref.: #66552]	galacturonate ChEBI	-	assimilation
[Ref.: #66552]	gelatin ChEBI	-	hydrolysis
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #66552]	gluconate ChEBI	+/-	growth
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #66552]	glucose ChEBI	+	carbon source
[Ref.: #66552]	glucose ChEBI	-	fermentation
[Ref.: #66552]	glucuronate ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #66552]	L-arginine ChEBI	-	hydrolysis
[Ref.: #66552]	lactate ChEBI	+/-	growth
[Ref.: #66552]	lactose ChEBI	+	carbon source
[Ref.: #66552]	lactulose ChEBI	+	carbon source
[Ref.: #66552]	laminarin ChEBI	+	hydrolysis
[Ref.: #66552]	leucrose ChEBI	+	carbon source
[Ref.: #66552]	lichenin ChEBI	+	hydrolysis
[Ref.: #66552]	malate ChEBI	+/-	growth
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #66552]	maltose ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #66552]	mannitol ChEBI	+/-	growth
[Ref.: #66552]	mannose ChEBI	+	carbon source
[Ref.: #66552]	melezitose ChEBI	+/-	growth
[Ref.: #66552]	melibiose ChEBI	+	carbon source
[Ref.: #66552]	methanol ChEBI	-	assimilation
[Ref.: #66552]	N-acetylglucosamine ChEBI	+/-	growth
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #66552]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #66552]	oxalate ChEBI	+	carbon source
[Ref.: #66552]	pectin ChEBI	-	hydrolysis
[Ref.: #66552]	peptone	+	hydrolysis
[Ref.: #66552]	propionate ChEBI	-	assimilation
[Ref.: #66552]	pullulan ChEBI	-	hydrolysis
[Ref.: #66552]	pyruvate ChEBI	+/-	growth
[Ref.: #66552]	raffinose ChEBI	+	carbon source
[Ref.: #66552]	rhamnose ChEBI	+	carbon source
[Ref.: #66552]	ribose ChEBI	+	carbon source
[Ref.: #66552]	salicin ChEBI	+	carbon source
[Ref.: #66552]	sorbitol ChEBI	-	assimilation
[Ref.: #66552]	sorbose ChEBI	-	assimilation
[Ref.: #66552]	starch ChEBI	-	hydrolysis
[Ref.: #66552]	succinate ChEBI	+	carbon source
[Ref.: #66552]	sucrose ChEBI	+	carbon source
[Ref.: #66552]	trehalose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #66552]	valerate ChEBI	-	assimilation
[Ref.: #66552]	xylan ChEBI	+	hydrolysis
[Ref.: #66552]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66552]		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.: #66552]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #66552]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #66552]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #66552]	alpha-fucosidase	-	3.2.1.51
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #66552]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #66552]	alpha-glucosidase	+	3.2.1.20
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #66552]	alpha-mannosidase	-	3.2.1.24
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #66552]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #66552]	beta-glucosidase	+	3.2.1.21
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE, API zym
[Ref.: #66552]	beta-glucuronidase	+	3.2.1.31
[Ref.: #68382]	beta-glucuronidase	+	3.2.1.31	* from API zym
[Ref.: #66552]	catalase	-	1.11.1.6
[Ref.: #66552]	cystine arylamidase	+	3.4.11.3
[Ref.: #66552]	cytochrome oxidase	+	1.9.3.1
[Ref.: #66552]	esterase	+
[Ref.: #66552]	esterase Lipase (C 8)	+
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #66552]	leucine arylamidase	+	3.4.11.1
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #66552]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #66552]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #66552]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #66552]	trypsin	-	3.4.21.4
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #66552]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #66552]	valine arylamidase	+
[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.: #64965]	24575	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.
[Ref.: #64965]	24573	-	-	-	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.

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.: #64965]	14005	-	+	+/-	+/-	-	+	+	+/-	-	+/-	+	+	-	+	+	-	+	+	-	-

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

[Ref.: #64965]	Sample type/isolated from	Lichen thalli (Cladonia sp.) collected from forested tundra
[Ref.: #64965]	Geographic location (country and/or sea, region)	West Siberia, Nadym region (65° 30'' 59' N, 72° 32'' 15' E)
[Ref.: #64965]	Country	Russia
[Ref.: #64965]	Country ISO 3 Code	RUS
[Ref.: #64965]	Continent	Asia
[Ref.: #64965]	Geographic location	65.5164°/72.5375°

[Ref.: #66552]	Sample type/isolated from	decomposed thalli of Cladonia sp.collected from the forested tundra
[Ref.: #66552]	Geographic location (country and/or sea, region)	Nadym Region, Yamalo-Nenets Autonomous Okrug
[Ref.: #66552]	Country	Russia
[Ref.: #66552]	Country ISO 3 Code	RUS
[Ref.: #66552]	Continent	Asia
[Ref.: #66552]	Geographic location	65.5164°/72.5375°
[Ref.: #66552]	Enrichment culture composition	Per liter: 0.25 g xylan, 0.25 g starch, 0.05 g Bacto Tryptic Soy Broth without dextrose, 0.1 g NH4NO3 , 0.04 g KH2PO4; pH was adjusted to 4.5 with 30 mg/l alginic acid; 9 g/l phytagel
[Ref.: #66552]	Enrichment culture duration	28 days
[Ref.: #66552]	Enrichment culture temperature	20 ̊C
[Ref.: #66552]	Isolation/enrichment procedure	collected thalli were ground in a mortar and resulting material was suspended in 5 ml sterile water
* marker position based on {}

Isolation sources categories

#Host

#Other

#Lichen

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.: #66552]	Edaphobacter lichenicola strain SBC68 16S ribosomal RNA gene, partial sequence	MG385062	1461	GenBank ENA	2051959 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Edaphobacter lichenicola DSM 104462	GCA_025264645	complete	GenBank ENA	2051959 tax ID	*
[Ref.: #66792]	Edaphobacter lichenicola strain DSM 104462	2051959.10	complete	PATRIC	2051959 tax ID	*

[Ref.: #66552]

GC-content

54.70 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Edaphobacter lichenicola DSM 104462 NCBI: GCA_025264645.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	88.947	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	94.64	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	82.236	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	79.635	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.805	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	50.787	no

Availability in culture collections External links

[Ref.: #64965]

Culture collection no.

DSM 104462, SBC 68, VKM B-3208

[Ref.: #111118]

SI-ID 397404

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Edaphobacter lichenicola sp. nov., a member of the family Acidobacteriaceae from lichen-dominated forested tundra.	Belova SE, Suzina NE, Rijpstra WIC, Sinninghe Damste JS, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijsem.0.002663	2018	*

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 )

#64965

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104462

#66552

Svetlana E. Belova, Natalia E. Suzina, W. Irene C. Rijpstra, Jaap S. Sinninghe Damsté and Svetlana N. Dedysh: Edaphobacter lichenicola sp. nov., a member of the family Acidobacteriaceae from lichen-dominated forested tundra. IJSEM 68: 1265 - 1270 2018 ( DOI 10.1099/ijsem.0.002663 , PubMed 29465339 )

#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 .

#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) .

#111118

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-ID397404.1 )

* These data were automatically processed and therefore are not curated

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