Sphingomonas edaphi (KCTC 62107, JCM 32377, DAC4)

Name: Sphingomonas edaphi (KCTC 62107, JCM 32377, DAC4)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164248

Type strain

Strain Designation DAC4

Culture col. no. KCTC 62107 JCM 32377 DAC4

NCBI tax ID(s) 2315689

Special Collections JCM KCTC Literature strains

History JCM <-- T. Seo; Dongguk Univ., South Korea; DAC4.

Links

Sphingomonas edaphi DAC4 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from Soil sample collected at Ahnmok Beach.

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

Name and taxonomic classification

SI-ID 26491

JCM 32377,KCTC 62107

@ref 20215

Last LPSN update 2026-05-29 08:45:22

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingomonas

Species Sphingomonas edaphi

Full scientific name Sphingomonas edaphi Kim et al. 2020

Synonyms (1)

Pseudosphingomonas edaphi

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
69545	negative	1.0-1.6 µm	0.4-0.7 µm	rod-shaped
125439	negative				95.381
125438	negative				94.6

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
69545	0.5-1.0 mm	yellow	circular	2 days	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
69545	Reasoner's 2A agar (R2A)

Culture temp

@ref	Growth	Type	Temperature (°C)
67770	positive	growth	30
69545	positive	growth	18-42
69545	positive	optimum	30

Culture pH

@ref	Ability	Type	PH
69545	positive	optimum	7
69545	positive	growth	6.0-9.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
69545	aerobe
125439	obligate aerobe	97.404

Spore formation

@ref	Spore formation	Confidence
125438		91.669
125439		98.687

Halophily

@ref	Salt	Growth	Tested relation	Concentration
69545	NaCl	positive	growth	0 %(w/v)
69545	NaCl	positive	optimum	0 %

Observation

@ref	Observation
67770	quinones: Q-10
69545	Strain DAC4T grew on R2A, nutrient agar and Luria-Bertani agar at 30 °C, but not on MacConkey agar or marine agar.
69545	The major polar lipids are diphosphatidylglycerol and sphingoglycolipids, and the predominant polyamine is HSPD.

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69545	16808 ChEBI	2-dehydro-D-gluconate	-	assimilation
69545	58143 ChEBI	5-dehydro-D-gluconate	+	assimilation
69545	17128 ChEBI	adipate	+	assimilation
69545	27613 ChEBI	amygdalin	-	assimilation
69545	18305 ChEBI	arbutin	-	assimilation
69545	17057 ChEBI	cellobiose	-	fermentation
69545	17108 ChEBI	D-arabinose	-	assimilation
69545	18333 ChEBI	D-arabitol	-	assimilation
69545	15824 ChEBI	D-fructose	-	assimilation
69545	28847 ChEBI	D-fucose	-	fermentation
69545	12936 ChEBI	D-galactose	-	assimilation
69545	17634 ChEBI	D-glucose	-	fermentation
69545	17634 ChEBI	D-glucose	+	assimilation
69545	62318 ChEBI	D-lyxose	-	assimilation
69545	16899 ChEBI	D-mannitol	-	assimilation
69545	16899 ChEBI	D-mannitol	+	assimilation
69545	16024 ChEBI	D-mannose	-	assimilation
69545	16988 ChEBI	D-ribose	-	assimilation
69545	17924 ChEBI	D-sorbitol	-	assimilation
69545	16443 ChEBI	D-tagatose	-	assimilation
69545	65327 ChEBI	D-xylose	-	assimilation
69545	27689 ChEBI	decanoate	-	assimilation
69545	17113 ChEBI	erythritol	-	assimilation
69545	4853 ChEBI	esculin	-	hydrolysis
69545	16813 ChEBI	galactitol	-	assimilation
69545	5291 ChEBI	gelatin	+	hydrolysis
69545	28066 ChEBI	gentiobiose	-	fermentation
69545	17234 ChEBI	glucose	-	fermentation
69545	17754 ChEBI	glycerol	-	assimilation
69545	28087 ChEBI	glycogen	+	fermentation
69545	15443 ChEBI	inulin	-	assimilation
69545	30849 ChEBI	L-arabinose	-	assimilation
69545	30849 ChEBI	L-arabinose	+	assimilation
69545	18403 ChEBI	L-arabitol	-	assimilation
69545	18287 ChEBI	L-fucose	-	assimilation
69545	62345 ChEBI	L-rhamnose	-	assimilation
69545	17266 ChEBI	L-sorbose	-	assimilation
69545	17716 ChEBI	lactose	-	assimilation
69545	25115 ChEBI	malate	-	assimilation
69545	17306 ChEBI	maltose	-	assimilation
69545	17306 ChEBI	maltose	+	assimilation
69545	6731 ChEBI	melezitose	-	assimilation
69545	28053 ChEBI	melibiose	-	assimilation
69545	320061 ChEBI	methyl alpha-D-glucopyranoside	-	assimilation
69545	43943 ChEBI	methyl alpha-D-mannoside	-	assimilation
69545	74863 ChEBI	methyl beta-D-xylopyranoside	-	assimilation
69545	17268 ChEBI	myo-inositol	-	assimilation
69545	506227 ChEBI	N-acetyl-D-glucosamine	+	assimilation
69545	17632 ChEBI	nitrate	-	reduction
69545	18401 ChEBI	phenylacetate	-	assimilation
69545	32032 ChEBI	potassium gluconate	+	assimilation
69545	16634 ChEBI	raffinose	-	assimilation
69545	15963 ChEBI	ribitol	-	assimilation
69545	17814 ChEBI	salicin	-	assimilation
69545	53258 ChEBI	sodium citrate	-	assimilation
69545	28017 ChEBI	starch	+	assimilation
69545	17992 ChEBI	sucrose	-	assimilation
69545	27082 ChEBI	trehalose	-	assimilation
69545	27897 ChEBI	tryptophan	-	energy source
69545	32528 ChEBI	turanose	-	fermentation
69545	17151 ChEBI	xylitol	+	fermentation

Metabolite production

@ref	Chebi-ID	Metabolite	Production
69545	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
69545	35581 ChEBI	indole	-

Enzymes

@ref	Value	Activity	Ec
69545	acid phosphatase	+	3.1.3.2
69545	alkaline phosphatase	+	3.1.3.1
69545	alpha-chymotrypsin	-	3.4.21.1
69545	alpha-fucosidase	-	3.2.1.51
69545	alpha-galactosidase	-	3.2.1.22
69545	alpha-glucosidase	+	3.2.1.20
69545	alpha-mannosidase	-	3.2.1.24
69545	arginine dihydrolase	-	3.5.3.6
69545	beta-galactosidase	-	3.2.1.23
69545	beta-glucosidase	-	3.2.1.21
69545	beta-glucuronidase	-	3.2.1.31
69545	catalase	+	1.11.1.6
69545	cystine arylamidase	+	3.4.11.3
69545	cytochrome oxidase	+	1.9.3.1
69545	esterase (C 4)	+
69545	esterase Lipase (C 8)	+
69545	leucine arylamidase	+	3.4.11.1
69545	lipase (C 14)	+
69545	N-acetyl-beta-glucosaminidase	-	3.2.1.52
69545	naphthol-AS-BI-phosphohydrolase	+
69545	trypsin	+	3.4.21.4
69545	tryptophan deaminase	-	4.1.99.1
69545	urease	-	3.5.1.5
69545	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

69545

Fatty acid	Percentage
C18:1 w7c	29.7
C16 :1 w7c/C16 :1 w6c	29.5
C16:0	11.7
C17:1 w6c	7.4
C18:1 2OH	5.9
C18:1 w7c 11-methyl	4.3
C16:1 w5c	3.3
C15:0	1.5
C17:1 w8c	1.3
C17:0	1.1
ante-C 18 :0/C18 :2 w6 ,9c	1
C18:0	0.6
C14:0 2OH	0.6
C18:1 w5c	0.5
C14:0	0.5
C15:1 H/C13:0 3OH	0.4
C14:1 w5c	0.4
C8:0 3OH	0.3

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
67770	Soil sample collected at Ahnmok Beach	Busan	Republic of Korea	KOR	Asia
69545	soil sample collected at Ahnmok Beach, Busan	Ahnmok Beach, Busan	Republic of Korea	KOR	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM358372v1 assembly for Sphingomonas edaphi DAC4	contig	GCA_003583725	2315689.3	2879151112	2315689	76.46

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Sphingomonas edaphi strain DAC4 16S ribosomal RNA gene, partial sequence	MF503624	1416		2315689

GC content

@ref	GC-content (mol%)	Method
67770	62.16	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM358372v1 assembly for Sphingomonas edaphi DAC4
NCBI: GCA_003583725

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.40	no
125439	motility	BacteriaNetⓘ	yes	47.51	no
125439	gram_stain	BacteriaNetⓘ	negative	95.38	no
125439	spore_formation	BacteriaNetⓘ	no	98.69	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sphingomonas edaphi DAC4
NCBI: GCA_003583725.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.60	no
125438	anaerobic	anaerobicⓘ	no	96.77	no
125438	aerobic	aerobicⓘ	yes	85.56	yes
125438	spore-forming	spore-formingⓘ	no	91.67	no
125438	thermophilic	thermophileⓘ	no	95.99	no
125438	flagellated	motile2+ⓘ	no	65.69	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingomonas xanthus sp. nov., Isolated from Beach Soil.	Kim H, Chhetri G, Seo T	Curr Microbiol	10.1007/s00284-020-02273-z	2020
Phylogeny	Sphingomonas edaphi sp. nov., a novel species isolated from beach soil in the Republic of Korea.	Kim H, Chhetri G, Seo T	Int J Syst Evol Microbiol	10.1099/ijsem.0.003780	2020

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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#69545	Hyungdong Kim, Geeta Chhetri and Taegun Seo: Sphingomonas edaphi sp. nov., a novel species isolated from beach soil in the Republic of Korea. IJSEM 70: 2019 ( DOI 10.1099/ijsem.0.003780 )
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Sphingomonas edaphi (KCTC 62107, JCM 32377, DAC4)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003583725

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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