Zobellella endophytica (ACCC 60074, KCTC 62456, 59N8)

Name: Zobellella endophytica (ACCC 60074, KCTC 62456, 59N8)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159772

Type strain

Strain Designation 59N8

Culture col. no. ACCC 60074 KCTC 62456 59N8

NCBI tax ID(s) 2116700

Special Collections KCTC Literature strains

History <- Lei Liu, Research Institute of Forestry, Chinese Academy of Forestry

Links

Zobellella endophytica 59N8 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from roots of Phragmites communis.

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

Name and taxonomic classification

SI-ID 286804

KCTC:62456

@ref 20215

Last LPSN update 2026-02-09 11:38:44

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Aeromonadales

Family Aeromonadaceae

Genus Zobellella

Species Zobellella endophytica

Full scientific name Zobellella endophytica Song et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
66768	negative	0.8-1.5 µm	0.4-0.6 µm	rod-shaped
125439	negative					99.7

Colony morphology

@ref	Colony color	Colony shape	Medium used
66768	white	circular	Marine agar (MA) 2216

Culture and growth conditions

Culture medium

@ref	Name	Growth
66768	Marine agar (MA) 2216

Culture temp

@ref	Growth	Type	Temperature (°C)
66768	positive	growth	10-45
66768	positive	optimum	25-37
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
66768	positive	optimum	7-8
66768	positive	growth	6-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
66768	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
66768
125439		99.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66768	NaCl	positive	growth	0-5 %
66768	NaCl	positive	optimum	0-4 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66768	28644 ChEBI	2-oxopentanoate	+	respiration
66768	37054 ChEBI	3-hydroxybutyrate	+	respiration
66768	16411 ChEBI	acetic acid	+	respiration
66768	17925 ChEBI	alpha-D-glucose	+	respiration
66768	22599 ChEBI	arabinose	-	fermentation
66768	73706 ChEBI	bromosuccinate	+	respiration
66768		casein	-	hydrolysis
66768	16383 ChEBI	cis-aconitate	+	respiration
66768	53258 ChEBI	citric acid	+	assimilation
66768	53258 ChEBI	citric acid	-	carbon source
66768	53258 ChEBI	citric acid	+	respiration
66768	15570 ChEBI	D-alanine	+	respiration
66768	15824 ChEBI	D-fructose	+	fermentation
66768	15824 ChEBI	D-fructose	+	respiration
66768	8391 ChEBI	D-gluconate	+	respiration
66768	17634 ChEBI	D-glucose	+	fermentation
66768	16899 ChEBI	D-mannitol	+	fermentation
66768	16899 ChEBI	D-mannitol	+	respiration
66768	4853 ChEBI	esculin	+	fermentation
66768	4853 ChEBI	esculin	+	hydrolysis
66768	16865 ChEBI	gamma-aminobutyric acid	+	respiration
66768	5291 ChEBI	gelatin	-	hydrolysis
66768	24265 ChEBI	gluconate	+	assimilation
66768	17234 ChEBI	glucose	+	assimilation
66768	17754 ChEBI	glycerol	+	fermentation
66768	17754 ChEBI	glycerol	+	respiration
66768	17596 ChEBI	inosine	+	respiration
66768	21217 ChEBI	L-alaninamide	+	respiration
66768	16977 ChEBI	L-alanine	+	respiration
66768	73786 ChEBI	L-alanylglycine	+	respiration
66768	17196 ChEBI	L-asparagine	+	respiration
66768	29991 ChEBI	L-aspartate	+	respiration
66768	29985 ChEBI	L-glutamate	+	respiration
66768	15971 ChEBI	L-histidine	+	respiration
66768	17203 ChEBI	L-proline	+	respiration
66768	17115 ChEBI	L-serine	+	respiration
66768	16857 ChEBI	L-threonine	+	respiration
66768	24996 ChEBI	lactate	+	respiration
66768	17716 ChEBI	lactose	+	respiration
66768	25115 ChEBI	malate	+	assimilation
66768	17306 ChEBI	maltose	+	assimilation
66768	17306 ChEBI	maltose	+	fermentation
66768	29864 ChEBI	mannitol	+	fermentation
66768	28053 ChEBI	melibiose	-	fermentation
66768	320055 ChEBI	methyl beta-D-glucopyranoside	+	respiration
66768	51850 ChEBI	methyl pyruvate	+	respiration
66768	17268 ChEBI	myo-inositol	-	fermentation
66768	17268 ChEBI	myo-inositol	+	respiration
66768	59640 ChEBI	N-acetylglucosamine	+	fermentation
66768	59640 ChEBI	N-acetylglucosamine	+	respiration
66768	17632 ChEBI	nitrate	+	reduction
66768	18401 ChEBI	phenylacetate	+	assimilation
66768	17272 ChEBI	propionate	+	respiration
66768	17148 ChEBI	putrescine	+	respiration
66768	26546 ChEBI	rhamnose	-	fermentation
66768	30911 ChEBI	sorbitol	-	fermentation
66768	28017 ChEBI	starch	-	hydrolysis
66768	30031 ChEBI	succinate	+	respiration
66768	17992 ChEBI	sucrose	+	fermentation
66768	17992 ChEBI	sucrose	+	respiration
66768	27082 ChEBI	trehalose	+	respiration
66768	32528 ChEBI	turanose	+	respiration
66768	27248 ChEBI	urocanic acid	+	respiration
66768	17151 ChEBI	xylitol	+	respiration

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66768	15688 ChEBI	acetoin
66768	16136 ChEBI	hydrogen sulfide

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
66768	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
66768	acid phosphatase	+	3.1.3.2
66768	alkaline phosphatase	+	3.1.3.1
66768	arginine dihydrolase	-	3.5.3.6
66768	catalase	+	1.11.1.6
66768	cytochrome oxidase	+	1.9.3.1
66768	esterase (C 4)	+
66768	esterase Lipase (C 8)	+
66768	leucine arylamidase	+	3.4.11.1
66768	lysine decarboxylase	-	4.1.1.18
66768	naphthol-AS-BI-phosphohydrolase	+
66768	ornithine decarboxylase	-	4.1.1.17
66768	urease	-	3.5.1.5
66768	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

66768

Fatty acid	Percentage
C18:1 w6c and/or C18:1 w7c	33.6
C16:1 w6c and/or C16:1 w7c	21.8
C16:0	15.8
C12:0	8.9
C14:0 3OH and/or iso-C16:1 I	8.8
C17:0 cyclo	4.3
C19:0 cyclo w8c	2.1
C16:0 3OH	1.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Isolation procedure
66768	roots of Phragmites communis	Phragmites communis	2013-08-30	Kumtag Desert in Xinjiang	China	CHN	Asia	40.4981	92.6542 40.4981/92.6542	nutrient agar and R2A	Root samples of Phragmites communis were collected, surface-sterilized and plated on nutrient agar medium (10.0 g l-1 peptone, 3.0 g l-1 beef extract, 5.0 g l-1 NaCl, and 15.0 g l-1 agar) and Reasoner's 2A agar medium.
67771	From Phragmites australis, Kumtag desert				China	CHN	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM301277v1 assembly for Zobellella endophytica 59N8	contig	GCA_003012775	2116700.3	2832216750	2116700	65.78

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66768	Zobellella endophytica strain 59N8 16S ribosomal RNA gene, partial sequence	MG706141	1466		2116700

GC content

@ref	GC-content (mol%)	Method
66768	62.8	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Zobellella endophytica 59N8
NCBI: GCA_003012775

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.40	no
125439	motility	BacteriaNetⓘ	yes	84.30	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	84.30	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Zobellella endophytica sp. nov., isolated from the roots of Phragmites communis in the Kumtag Desert.	Song Z, Sun QW, Liang LX, Zhang XX, Li LB, Liu L	Int J Syst Evol Microbiol	10.1099/ijsem.0.003064	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 )
#66768	Zheng Song, Qi-wu Sun, Li-xiong Liang, Xiao-xia Zhang, Lu-bin Li, Lei Liu: Zobellella endophytica sp. nov., isolated from the roots of Phragmites communis in the Kumtag Desert. IJSEM 68: 3807 - 3811 2018 ( DOI 10.1099/ijsem.0.003064 , PubMed 30311869 )
#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;
#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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Zobellella endophytica (ACCC 60074, KCTC 62456, 59N8)

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

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003012775

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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