Name: Edaphobacter bradus 4MSH08
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 159869

Type strain:

Species: Edaphobacter bradus

Strain Designation: 4MSH08

Culture col. no.: GDMCC 1.1317, KCTC 62475

Strain history: <- Lihong Qiu, Sun Sat-Sen Univ.

NCBI tax ID(s): 2259016 (species)

Special Collections

Section

Edaphobacter bradus 4MSH08 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from forest soil.

colony-forming
Gram-negative
rod-shaped
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 bradus**
	Full Scientific Name (LPSN)	Edaphobacter bradus Xia et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66613]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative

[Ref.: #66613]	Cell length	1.3-1.8 µm

[Ref.: #66613]	Cell width	0.6-0.9 µm

[Ref.: #66613]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #66613]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #66613]	Colony color	canary yellow
[Ref.: #66613]	Colony shape	circular
[Ref.: #66613]	Incubation period	14 days
[Ref.: #66613]	Cultivation medium used	1:10 diluted HD medium

Information on culture and growth conditions Culture and growth conditions

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Culture medium

1:10 diluted HD medium

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Culture medium growth

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Culture medium

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Culture medium growth

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #66613]	optimum	28 °C
[Ref.: #66613]	growth	10-37 °C
[Ref.: #67771]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #66613]			optimum	4.0-5.5
[Ref.: #66613]			growth	3.0-6.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66613]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66613]		NaCl		growth	0-3.0	%(w/v)

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Observation

binary fission

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66613]	adipate ChEBI	+	assimilation
[Ref.: #66613]	amygdalin ChEBI	-	assimilation
[Ref.: #66613]	arbutin ChEBI	+	assimilation
[Ref.: #66613]	arginine ChEBI	+	hydrolysis
[Ref.: #66613]	cellobiose ChEBI	-	assimilation
[Ref.: #66613]	D-arabinose ChEBI	-	assimilation
[Ref.: #66613]	D-arabitol ChEBI	-	assimilation
[Ref.: #66613]	D-fructose ChEBI	+	assimilation
[Ref.: #66613]	D-fucose ChEBI	+	assimilation
[Ref.: #66613]	D-galactose ChEBI	-	assimilation
[Ref.: #66613]	D-glucose ChEBI	-	assimilation
[Ref.: #66613]	D-lyxose ChEBI	-	assimilation
[Ref.: #66613]	D-mannitol ChEBI	+	assimilation
[Ref.: #66613]	D-mannose ChEBI	-	assimilation
[Ref.: #66613]	D-ribose ChEBI	-	assimilation
[Ref.: #66613]	D-sorbitol ChEBI	-	assimilation
[Ref.: #66613]	D-tagatose ChEBI	+	assimilation
[Ref.: #66613]	D-xylose ChEBI	-	assimilation
[Ref.: #66613]	decanoate ChEBI	-	assimilation
[Ref.: #66613]	erythritol ChEBI	-	assimilation
[Ref.: #66613]	esculin ChEBI	+	hydrolysis
[Ref.: #66613]	esculin ferric citrate	+	assimilation
[Ref.: #66613]	galactitol ChEBI	-	assimilation
[Ref.: #66613]	gelatin ChEBI	-	hydrolysis
[Ref.: #66613]	gentiobiose ChEBI	-	assimilation
[Ref.: #66613]	glucose ChEBI	+	fermentation
[Ref.: #66613]	glycerol ChEBI	-	assimilation
[Ref.: #66613]	glycogen ChEBI	+	assimilation
[Ref.: #66613]	inulin ChEBI	+	assimilation
[Ref.: #66613]	L-arabinose ChEBI	+	assimilation
[Ref.: #66613]	L-arabitol ChEBI	-	assimilation
[Ref.: #66613]	L-fucose ChEBI	-	assimilation
[Ref.: #66613]	L-rhamnose ChEBI	-	assimilation
[Ref.: #66613]	L-sorbose ChEBI	-	assimilation
[Ref.: #66613]	L-xylose ChEBI	+	assimilation
[Ref.: #66613]	lactose ChEBI	+	assimilation
[Ref.: #66613]	malate ChEBI	-	assimilation
[Ref.: #66613]	maltose ChEBI	-	assimilation
[Ref.: #66613]	maltose ChEBI	+	assimilation
[Ref.: #66613]	melezitose ChEBI	+	assimilation
[Ref.: #66613]	melibiose ChEBI	-	assimilation
[Ref.: #66613]	methyl alpha-D-glucopyranoside ChEBI	+	assimilation
[Ref.: #66613]	methyl alpha-D-mannoside ChEBI	+	assimilation
[Ref.: #66613]	methyl beta-D-xylopyranoside ChEBI	-	assimilation
[Ref.: #66613]	myo-inositol ChEBI	-	assimilation
[Ref.: #66613]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #66613]	nitrate ChEBI	-	reduction
[Ref.: #66613]	phenylacetate ChEBI	-	assimilation
[Ref.: #66613]	potassium 2-dehydro-D-gluconate	-	assimilation
[Ref.: #66613]	potassium 5-dehydro-D-gluconate	-	assimilation
[Ref.: #66613]	potassium gluconate ChEBI	-	assimilation
[Ref.: #66613]	raffinose ChEBI	+	assimilation
[Ref.: #66613]	ribitol ChEBI	-	assimilation
[Ref.: #66613]	salicin ChEBI	-	assimilation
[Ref.: #66613]	starch ChEBI	-	assimilation
[Ref.: #66613]	starch ChEBI	+	hydrolysis
[Ref.: #66613]	sucrose ChEBI	-	assimilation
[Ref.: #66613]	trehalose ChEBI	-	assimilation
[Ref.: #66613]	turanose ChEBI	+	assimilation
[Ref.: #66613]	xylitol ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #66613]		hydrogen sulfide ChEBI	yes
[Ref.: #66613]		indole ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #66613]	acid phosphatase	-	3.1.3.2
[Ref.: #66613]	alkaline phosphatase	+	3.1.3.1
[Ref.: #66613]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #66613]	alpha-fucosidase	+	3.2.1.51
[Ref.: #66613]	alpha-galactosidase	+	3.2.1.22
[Ref.: #66613]	alpha-glucosidase	+	3.2.1.20
[Ref.: #66613]	alpha-mannosidase	+	3.2.1.24
[Ref.: #66613]	beta-galactosidase	+	3.2.1.23
[Ref.: #66613]	beta-glucosidase	+	3.2.1.21
[Ref.: #66613]	beta-glucuronidase	+	3.2.1.31
[Ref.: #66613]	catalase	+	1.11.1.6
[Ref.: #66613]	cystine arylamidase	+	3.4.11.3
[Ref.: #66613]	cytochrome oxidase	-	1.9.3.1
[Ref.: #66613]	esterase (C 4)	-
[Ref.: #66613]	esterase Lipase (C 8)	-
[Ref.: #66613]	leucine arylamidase	+	3.4.11.1
[Ref.: #66613]	lipase (C 14)	-
[Ref.: #66613]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #66613]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #66613]	trypsin	-	3.4.21.4
[Ref.: #66613]	urease	+	3.5.1.5
[Ref.: #66613]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #66613]	Sample type/isolated from	forest soil
[Ref.: #66613]	Geographic location (country and/or sea, region)	Dinghushan Biosphere Reserve, Guangdong Province
[Ref.: #66613]	Country	China
[Ref.: #66613]	Country ISO 3 Code	CHN
[Ref.: #66613]	Continent	Asia
[Ref.: #66613]	Geographic location	23.1667°/112.5170°
[Ref.: #66613]	Enrichment culture	MM1F
[Ref.: #66613]	Enrichment culture composition	0.04 g MgSO4 . 7H2O, 0.02 g CaCl2 . 2H2O, 0.05 g yeast extract, 0.5 g fructose, 15 g agar in 1 litre of distilled water, pH 5.0
[Ref.: #66613]	Enrichment culture duration	14 days
[Ref.: #66613]	Enrichment culture temperature	28 ̊C
[Ref.: #66613]	Isolation/enrichment procedure	soil sample was thoroughly suspended with 100 mM phosphate buffered saline, 1:10 diluted three times and plated on MM1F agar medium

[Ref.: #67771]	Sample type/isolated from	From forest soil
[Ref.: #67771]	Geographic location (country and/or sea, region)	Dinghushan Biosphere Reserve, Guangdong Province
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
[Ref.: #67771]	Geographic location	23.1667°/112.5170°
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

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.: #66613]	Edaphobacter bradus strain 4MSH08 16S ribosomal RNA gene, partial sequence	MF150299	1464	GenBank ENA	2259016 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Edaphobacter bradus 4MSH08	GCA_025685645	contig	GenBank ENA	2259016 tax ID	*

[Ref.: #66613]	GC-content	59.60 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	59.6 mol%

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 bradus 4MSH08 NCBI: GCA_025685645.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	88.996	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	89.484	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	81.207	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	84.568	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	92.707	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	56.273	no

Availability in culture collections External links

[Ref.: #66613]

Culture collection no.

GDMCC 1.1317, KCTC 62475

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Edaphobacter flagellatus sp. nov. and Edaphobacter bradus sp. nov., two acidobacteria isolated from forest soil.	Xia F, Ou-Yang TN, Gao ZH, Qiu LH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002871	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 )

#66613

Fan Xia, Tian-na Ou-yang, Zeng-hong Gao and Li-hong Qiu: Edaphobacter flagellatus sp. nov. and Edaphobacter bradus sp. nov., two acidobacteria isolated from forest soil. IJSEM 68: 2530 - 2537 2018 ( DOI 10.1099/ijsem.0.002871 , PubMed 29957171 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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) .

* These data were automatically processed and therefore are not curated

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