Name: Edaphobacter lichenicola DSM 104462
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/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

Section

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

Gram-negative
rod-shaped
mesophilic
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

[Ref.: #64965]

Temperature range

mesophilic

	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	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	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	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Edaphobacter lichenicola DSM 104462 NCBI: GCA_025264645.1
[Ref.: #69480]	motile	no	65.395	yes
[Ref.: #69480]	flagellated	no	87.432	yes
[Ref.: #69480]	gram-positive	no	96.701	yes
[Ref.: #69480]	anaerobic	no	99.042	no
[Ref.: #69480]	aerobic	yes	87.823	no
[Ref.: #69480]	halophile	no	94.624	yes
[Ref.: #69480]	spore-forming	no	89.261	no
[Ref.: #69480]	glucose-ferment	no	91.519	no
[Ref.: #69480]	thermophile	no	98.171	yes
[Ref.: #69480]	glucose-util	yes	69.714	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

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 Edaphobacter lichenicola in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF