Name: Egibacter rhizosphaerae CGMCC 1.14997
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 141132

Type strain:

Species: Egibacter rhizosphaerae

Culture col. no.: CGMCC 1.14997, KCTC 39588, EGI 80759

Strain history: <- Wenjun Li

NCBI tax ID(s): 1670831 (species)

Special Collections

Section

Egibacter rhizosphaerae CGMCC 1.14997 is an aerobe, haloalkaliphilic, chemoorganotroph bacterium that forms irregular colonies and was isolated from rhizosphere soil sample of Tamarix hispida.

colony-forming
Gram-positive
rod-shaped
aerobe
chemoorganotroph
haloalkaliphilic
16S sequence
Bacteria

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Nitriliruptoria*
	Order	*Egibacterales*
	Family	*Egibacteraceae*
	Genus	*Egibacter*
	Species	**Egibacter rhizosphaerae**
	Full Scientific Name (LPSN)	Egibacter rhizosphaerae Zhang et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #44045]	Gram stain	positive

[Ref.: #44045]	Cell length	1.0-1.3 µm

[Ref.: #44045]	Cell width	0.3-0.4 µm

[Ref.: #44045]	Cell shape	rod-shaped

[Ref.: #44045]	Motility	no

[Ref.: #44045]	Colony color	pale-yellow
[Ref.: #44045]	Colony shape	irregular
[Ref.: #44045]	Incubation period	28 days
[Ref.: #44045]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #44045]

Culture medium

PDA

[Ref.: #44045]

Culture medium growth

[Ref.: #44045]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #44045]

Culture medium growth

		Temperature
[Ref.: #44045]	growth	25-50 °C
[Ref.: #44045]	optimum	30-35 °C
[Ref.: #67771]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #44045]			optimum	9.0-10.0
[Ref.: #44045]			growth	7.0-11.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #44045]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #44045]

Nutrition type

chemoorganotroph

[Ref.: #44045]	Type of spore	endospore
[Ref.: #44045]	Ability of spore formation	no

[Ref.: #44045]

Halophily / tolerance level

haloalkaliphilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #44045]		NaCl		growth	8-25	%(w/v)
[Ref.: #44045]		NaCl		optimum	10-12	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #44045]	casein	-	hydrolysis
[Ref.: #44045]	cellobiose ChEBI	+	carbon source
[Ref.: #44045]	cellulose ChEBI	-	hydrolysis
[Ref.: #44045]	D-arabinose ChEBI	+	carbon source
[Ref.: #44045]	D-fructose ChEBI	+	carbon source
[Ref.: #44045]	D-galactose ChEBI	+	carbon source
[Ref.: #44045]	D-glucose ChEBI	-	carbon source
[Ref.: #44045]	D-mannitol ChEBI	+	carbon source
[Ref.: #44045]	D-mannose ChEBI	+	carbon source
[Ref.: #44045]	D-ribose ChEBI	+	carbon source
[Ref.: #44045]	D-sorbitol ChEBI	+	carbon source
[Ref.: #44045]	D-xylose ChEBI	+	carbon source
[Ref.: #44045]	galactitol ChEBI	+	carbon source
[Ref.: #44045]	glycerol ChEBI	+	carbon source
[Ref.: #44045]	glycine ChEBI	-	nitrogen source
[Ref.: #44045]	hypoxanthine ChEBI	+	nitrogen source
[Ref.: #44045]	L-alanine ChEBI	-	nitrogen source
[Ref.: #44045]	L-arabinose ChEBI	+	carbon source
[Ref.: #44045]	L-arginine ChEBI	+	nitrogen source
[Ref.: #44045]	L-aspartate ChEBI	+	nitrogen source
[Ref.: #44045]	L-cysteine ChEBI	-	nitrogen source
[Ref.: #44045]	L-glutamate ChEBI	-	nitrogen source
[Ref.: #44045]	L-glutamine ChEBI	-	nitrogen source
[Ref.: #44045]	L-histidine ChEBI	+	nitrogen source
[Ref.: #44045]	L-isoleucine ChEBI	+	nitrogen source
[Ref.: #44045]	L-leucine ChEBI	+	nitrogen source
[Ref.: #44045]	L-lysine ChEBI	-	nitrogen source
[Ref.: #44045]	L-methionine ChEBI	-	nitrogen source
[Ref.: #44045]	L-phenylalanine ChEBI	+	nitrogen source
[Ref.: #44045]	L-proline ChEBI	-	nitrogen source
[Ref.: #44045]	L-rhamnose ChEBI	+	carbon source
[Ref.: #44045]	L-serine ChEBI	+	nitrogen source
[Ref.: #44045]	L-threonine ChEBI	-	nitrogen source
[Ref.: #44045]	L-tryptophan ChEBI	+	nitrogen source
[Ref.: #44045]	L-tyrosine ChEBI	-	nitrogen source
[Ref.: #44045]	L-valine ChEBI	+	nitrogen source
[Ref.: #44045]	lactose ChEBI	+	carbon source
[Ref.: #44045]	maltose ChEBI	+	carbon source
[Ref.: #44045]	myo-inositol ChEBI	+	carbon source
[Ref.: #44045]	nitrate ChEBI	+	reduction
[Ref.: #44045]	sodium acetate ChEBI	+	carbon source
[Ref.: #44045]	sodium citrate ChEBI	+	carbon source
[Ref.: #44045]	starch ChEBI	-	hydrolysis
[Ref.: #44045]	sucrose ChEBI	+	carbon source
[Ref.: #44045]	trehalose ChEBI	+	carbon source
[Ref.: #44045]	tryptophan ChEBI	-	hydrolysis
[Ref.: #44045]	tween 20 ChEBI	-	hydrolysis
[Ref.: #44045]	tween 40 ChEBI	+	hydrolysis
[Ref.: #44045]	tween 60 ChEBI	-	hydrolysis
[Ref.: #44045]	tween 80 ChEBI	+	hydrolysis
[Ref.: #44045]	xylitol ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #44045]		hydrogen sulfide ChEBI	no

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #44045]		catalase	+	1.11.1.6

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #44045]

Fatty acid	Percentage
10-Methyl C17:0	32
C17:1ω8c	22.1
C17:0	11.1
C16:0	7.9
iso-C17:1ω9c / 10-methyl-C16:0	4.7
C16:0 iso	4.2
C17:1ω6c	3.7
C16:1ω7c / C16:1ω6c / C16:1ω6c /	2
C15:1ω8c	1.7
C17:0 iso	1.4
C16:1ω9c	1.4
C15:1ω6c	1.3
C17:0 anteiso	1.2
10-Methyl C18:0	1
iso-C16:1-H	1
C18:1ω7c / C18:1ω6c	0.6
C18:0	0.6
C18:1ω9c	0.5
C15:0 iso	0.5
C18:2ω6,9c / anteiso-C18:0 / anteiso-C18:0 /	0.4
C14:0	0.4
C18:3ω6c	0.4
C15:0 anteiso	0.2

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	resorcinol degradation	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	phenylmercury acetate degradation	100	2 of 2
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	ethylmalonyl-CoA pathway	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	creatinine degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	myo-inositol biosynthesis	90	9 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	purine metabolism	82.98	78 of 94
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	pyrimidine metabolism	80	36 of 45
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	tryptophan metabolism	78.95	30 of 38
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	degradation of pentoses	78.57	22 of 28
[Ref.: #66794]	4-hydroxymandelate degradation	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	degradation of hexoses	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	non-pathway related	71.05	27 of 38
[Ref.: #66794]	4-hydroxyphenylacetate degradation	70	7 of 10
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	sulfoquinovose degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	phenol degradation	60	12 of 20
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	heme metabolism	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	allantoin degradation	55.56	5 of 9
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	chlorophyll metabolism	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
		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.: #44045]	Sample type/isolated from	rhizosphere soil sample of Tamarix hispida
[Ref.: #44045]	Sampling date	2013-07
[Ref.: #44045]	Geographic location (country and/or sea, region)	Karamay, Xinjiang Province
[Ref.: #44045]	Country	China
[Ref.: #44045]	Country ISO 3 Code	CHN
[Ref.: #44045]	Continent	Asia
[Ref.: #44045]	Enrichment culture	modified R2A
[Ref.: #44045]	Enrichment culture composition	with 10 % NaCl (w/v) and pH 10
[Ref.: #44045]	Enrichment culture duration	28 days
[Ref.: #44045]	Enrichment culture temperature	30 ̊C

[Ref.: #67771]	Sample type/isolated from	Desert soil
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Shrub (Scrub)
#Host Body-Site	#Plant	#Rhizosphere

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KR605111 (>99% sequence identity) for Egibacter rhizosphaerae subclade from Microbeatlas

Aquatic Samples	44
Soil Samples	121
Animal Samples	17
Plant Samples	2
Total Samples	184

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.: #44045]	Egibacter rhizosphaerae strain EGI 80759 16S ribosomal RNA gene, partial sequence	KR605111		GenBank ENA

[Ref.: #44045]

GC-content

72.1 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #44045]

Culture collection no.

CGMCC 1.14997, KCTC 39588, EGI 80759

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative genomics analysis of Nitriliruptoria reveals the genomic differences and salt adaptation strategies.	Chen DD, Tian Y, Jiao JY, Zhang XT, Zhang YG, Dong ZY, Xiong MJ, Xiao M, Shu WS, Li WJ	Extremophiles	10.1007/s00792-019-01150-3	2019	*
Phylogeny	Egibacter rhizosphaerae gen. nov., sp. nov., an obligately halophilic, facultatively alkaliphilic actinobacterium and proposal of Egibaceraceae fam. nov. and Egibacterales ord. nov.	Zhang YG, Wang HF, Yang LL, Zhou XK, Zhi XY, Duan YQ, Xiao M, Zhang YM, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.000713	2015	*

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 )

#44045

Yong-Guang Zhang, Hong-Fei Wang, Ling-Ling Yang, Xing-Kui Zhou, Xiao-Yang Zhi, Yan-Qing Duan, Min Xiao, Yuan-Ming Zhang and Wen-Jun Li: Egibacter rhizosphaerae gen. nov., sp. nov., an obligately halophilic, facultatively alkaliphilic actinobacterium and proposal of Egibaceraceae fam. nov. and Egibacterales ord. nov.. IJSEM 66: 283 - 289 2016 ( DOI 10.1099/ijsem.0.000713 , PubMed 26510781 )

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

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

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

* These data were automatically processed and therefore are not curated

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