Name: Rhizobium ipomoeae shin9-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140867

Type strain:

Species: Rhizobium ipomoeae

Strain Designation: shin9-1

Culture col. no.: LMG 27163, KCTC 32148

NCBI tax ID(s): 1210932 (species)

Section

Rhizobium ipomoeae shin9-1 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from Water convolvulus field.

colony-forming
Gram-negative
motile
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Rhizobiaceae*
	Genus	*Rhizobium*
	Species	**Rhizobium ipomoeae**
	Full Scientific Name (LPSN)	Rhizobium ipomoeae Sheu et al. 2016

Synonym

Peteryoungia ipomoeae

Information on morphological and physiological properties Morphology

[Ref.: #43690]	Gram stain	negative

[Ref.: #43690]	Cell length	1-1.5 µm

[Ref.: #43690]	Cell width	0.2-0.3 µm

[Ref.: #43690]	Cell shape	rod-shaped

[Ref.: #43690]	Motility	yes

[Ref.: #43690]	Flagellum arrangement	monotrichous, polar

[Ref.: #43690]	Colony size	1-1.2 mm
[Ref.: #43690]	Colony color	Cream-coloured
[Ref.: #43690]	Colony shape	circular
[Ref.: #43690]	Incubation period	2 days
[Ref.: #43690]	Cultivation medium used	R2A agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43690]

Culture medium

Reasoner's 2A agar (R2A)

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Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #43690]			growth	10-45 °C
[Ref.: #43690]			optimum	30 °C

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Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #43690]			optimum	7
[Ref.: #43690]			growth	7-9

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

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Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43690]		NaCl		growth	0-3	%
[Ref.: #43690]		NaCl		optimum	0.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43690]	2-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #43690]	2-oxobutanoate ChEBI	+	carbon source
[Ref.: #43690]	adipate ChEBI	-	assimilation
[Ref.: #43690]	alginate ChEBI	-	hydrolysis
[Ref.: #43690]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #43690]	alpha-lactose ChEBI	+	carbon source
[Ref.: #43690]	arabinose ChEBI	+	assimilation
[Ref.: #43690]	beta-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #43690]	bromosuccinate ChEBI	+	carbon source
[Ref.: #43690]	carboxymethylcellulose ChEBI	-	hydrolysis
[Ref.: #43690]	casein	-	hydrolysis
[Ref.: #43690]	cellobiose ChEBI	+	carbon source
[Ref.: #43690]	chitin ChEBI	-	hydrolysis
[Ref.: #43690]	cis-aconitate ChEBI	+	carbon source
[Ref.: #43690]	citrate ChEBI	+	assimilation
[Ref.: #43690]	citrate ChEBI	+	carbon source
[Ref.: #43690]	corn oil	-	hydrolysis
[Ref.: #43690]	D-arabitol ChEBI	+	carbon source
[Ref.: #43690]	D-fructose ChEBI	+	carbon source
[Ref.: #43690]	D-galactose ChEBI	+	carbon source
[Ref.: #43690]	D-gluconate ChEBI	+	carbon source
[Ref.: #43690]	D-glucose ChEBI	-	builds acid from
[Ref.: #43690]	D-glucose 6-phosphate ChEBI	+	carbon source
[Ref.: #43690]	D-mannitol ChEBI	+	carbon source
[Ref.: #43690]	D-mannose ChEBI	+	carbon source
[Ref.: #43690]	D-psicose ChEBI	+	carbon source
[Ref.: #43690]	D-serine ChEBI	+	carbon source
[Ref.: #43690]	D-sorbitol ChEBI	+	carbon source
[Ref.: #43690]	decanoate ChEBI	-	assimilation
[Ref.: #43690]	dextrin ChEBI	+	carbon source
[Ref.: #43690]	DL-carnitine ChEBI	+	carbon source
[Ref.: #43690]	dna ChEBI	-	hydrolysis
[Ref.: #43690]	erythritol ChEBI	+	carbon source
[Ref.: #43690]	esculin ChEBI	+	hydrolysis
[Ref.: #43690]	gelatin ChEBI	-	hydrolysis
[Ref.: #43690]	gentiobiose ChEBI	+	carbon source
[Ref.: #43690]	gluconate ChEBI	+	assimilation
[Ref.: #43690]	glucose ChEBI	-	fermentation
[Ref.: #43690]	glucose ChEBI	+	assimilation
[Ref.: #43690]	glucose 1-phosphate ChEBI	+	carbon source
[Ref.: #43690]	glycerol ChEBI	+	carbon source
[Ref.: #43690]	glycogen ChEBI	+	carbon source
[Ref.: #43690]	glycyl L-aspartic acid ChEBI	+	carbon source
[Ref.: #43690]	glycyl-l-glutamate ChEBI	+	carbon source
[Ref.: #43690]	hydroxyproline ChEBI	+	carbon source
[Ref.: #43690]	inosine ChEBI	+	carbon source
[Ref.: #43690]	L-alanine 4-nitroanilide	+	carbon source
[Ref.: #43690]	L-alanylglycine ChEBI	+	carbon source
[Ref.: #43690]	L-arabinose ChEBI	+	carbon source
[Ref.: #43690]	L-asparagine ChEBI	+	carbon source
[Ref.: #43690]	L-aspartate ChEBI	+	carbon source
[Ref.: #43690]	L-fucose ChEBI	+	carbon source
[Ref.: #43690]	L-glutamate ChEBI	+	carbon source
[Ref.: #43690]	L-rhamnose ChEBI	+	carbon source
[Ref.: #43690]	L-serine ChEBI	+	carbon source
[Ref.: #43690]	lactate ChEBI	+	carbon source
[Ref.: #43690]	lecithin ChEBI	-	hydrolysis
[Ref.: #43690]	malate ChEBI	-	assimilation
[Ref.: #43690]	maltose ChEBI	+	assimilation
[Ref.: #43690]	maltose ChEBI	+	carbon source
[Ref.: #43690]	mannitol ChEBI	+	assimilation
[Ref.: #43690]	mannose ChEBI	+	assimilation
[Ref.: #43690]	melibiose ChEBI	+	carbon source
[Ref.: #43690]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #43690]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #43690]	monomethyl succinate ChEBI	+	carbon source
[Ref.: #43690]	myo-inositol ChEBI	+	carbon source
[Ref.: #43690]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #43690]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #43690]	nitrate ChEBI	+	reduction
[Ref.: #43690]	phenylacetate ChEBI	-	assimilation
[Ref.: #43690]	propionate ChEBI	+	carbon source
[Ref.: #43690]	quinate ChEBI	+	carbon source
[Ref.: #43690]	raffinose ChEBI	+	carbon source
[Ref.: #43690]	starch ChEBI	-	hydrolysis
[Ref.: #43690]	succinamate ChEBI	+	carbon source
[Ref.: #43690]	sucrose ChEBI	+	carbon source
[Ref.: #43690]	thymidine ChEBI	+	carbon source
[Ref.: #43690]	trehalose ChEBI	+	carbon source
[Ref.: #43690]	turanose ChEBI	+	carbon source
[Ref.: #43690]	tween 20 ChEBI	+	hydrolysis
[Ref.: #43690]	tween 40 ChEBI	-	hydrolysis
[Ref.: #43690]	tween 40 ChEBI	+	carbon source
[Ref.: #43690]	tween 60 ChEBI	-	hydrolysis
[Ref.: #43690]	tween 80 ChEBI	-	hydrolysis
[Ref.: #43690]	tween 80 ChEBI	+	carbon source
[Ref.: #43690]	urea ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43690]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #43690]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #43690]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #43690]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #43690]	nalidixic acid ChEBI	yes	30	µg (disc)
[Ref.: #43690]	novobiocin ChEBI	yes	30	µg (disc)
[Ref.: #43690]	penicillin g ChEBI	yes	10	Unit (disc)
[Ref.: #43690]	rifampicin ChEBI	yes	5	µg (disc)
[Ref.: #43690]	streptomycin ChEBI	yes	10	µg (disc)
[Ref.: #43690]	sulfamethoxazole ChEBI				yes	23.75	µg (disc)
[Ref.: #43690]	tetracycline ChEBI	yes	30	µg (disc)
[Ref.: #43690]	trimethoprim ChEBI				yes	1.25	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43690]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43690]	acid phosphatase	+	3.1.3.2
[Ref.: #43690]	alkaline phosphatase	+	3.1.3.1
[Ref.: #43690]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #43690]	alpha-fucosidase	-	3.2.1.51
[Ref.: #43690]	alpha-galactosidase	+	3.2.1.22
[Ref.: #43690]	alpha-glucosidase	+	3.2.1.20
[Ref.: #43690]	alpha-mannosidase	-	3.2.1.24
[Ref.: #43690]	arginine dihydrolase	-	3.5.3.6
[Ref.: #43690]	beta-galactosidase	+	3.2.1.23
[Ref.: #43690]	beta-glucuronidase	-	3.2.1.31
[Ref.: #43690]	catalase	+	1.11.1.6
[Ref.: #43690]	cystine arylamidase	-	3.4.11.3
[Ref.: #43690]	cytochrome oxidase	+	1.9.3.1
[Ref.: #43690]	esterase (C 4)	+
[Ref.: #43690]	esterase Lipase (C 8)	+
[Ref.: #43690]	leucine arylamidase	+	3.4.11.1
[Ref.: #43690]	lipase (C 14)	-
[Ref.: #43690]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #43690]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #43690]	trypsin	+	3.4.21.4
[Ref.: #43690]	urease	+	3.5.1.5
[Ref.: #43690]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43690]

Fatty acid	Percentage
C16:0 iso	70.9
10-methyl C17:0	11.2
C16:1 iso H	4.2
C14:0 iso	3.4
C16:0 / iso-C17:1ω9c	2.5
C17:1ω8c	1.7
C16:0	0.8
C15:0 iso	0.7
C18:0 iso	0.7
C17:0	0.5
C17:0 anteiso	0.5

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

[Ref.: #43690]	Sample type/isolated from	Water convolvulus (Ipomoea aquatica) field
[Ref.: #43690]	Geographic location (country and/or sea, region)	Taitung city
[Ref.: #43690]	Country	Taiwan
[Ref.: #43690]	Country ISO 3 Code	TWN
[Ref.: #43690]	Continent	Asia
[Ref.: #43690]	Geographic location	22.9570°/121.1570°
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Environmental	#Aquatic	-
#Host	#Plants	#Aquatic plant
#Host	#Plants	#Herbaceous plants (Grass,Crops)

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.: #43690]	16S rRNA gene sequence	HE866935		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Peteryoungia ipomoeae shin9-1	GCA_004912165	contig	GenBank	1210932 tax ID	*

[Ref.: #43690]

GC-content

58.3 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizobium ipomoeae shin9-1 NCBI: GCA_004912165.1
[Ref.: #69480]	motile	yes	90.408	yes
[Ref.: #69480]	flagellated	yes	62.98	yes
[Ref.: #69480]	gram-positive	no	98.701	no
[Ref.: #69480]	anaerobic	no	96.948	no
[Ref.: #69480]	aerobic	yes	90.862	yes
[Ref.: #69480]	halophile	no	87.23	no
[Ref.: #69480]	spore-forming	no	96.003	no
[Ref.: #69480]	glucose-util	yes	93.277	no
[Ref.: #69480]	thermophile	no	98.214	yes
[Ref.: #69480]	glucose-ferment	no	91.211	no

Availability in culture collections External links

[Ref.: #43690]

Culture collection no.

LMG 27163, KCTC 32148

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium setariae sp. nov., an Indole-3-Acetic Acid-Producing Bacterium Isolated from Green Foxtail, Setaria viridis.	Kang M, Seo T	Curr Microbiol	10.1007/s00284-022-02860-2	2022	*
Phylogeny	Peteryoungia gen. nov. with four new species combinations and description of Peteryoungia desertarenae sp. nov., and taxonomic revision of the genus Ciceribacter based on phylogenomics of Rhizobiaceae.	Rahi P, Khairnar M, Hagir A, Narayan A, Jain KR, Madamwar D, Pansare A, Shouche Y	Arch Microbiol	10.1007/s00203-021-02349-9	2021	*
Phylogeny	Rhizobium rhizophilum sp. nov., an indole acetic acid-producing bacterium isolated from rape (Brassica napus L.) rhizosphere soil.	Gao JL, Wang LW, Xue J, Tong S, Peng G, Sun YC, Zhang X, Sun JG	Int J Syst Evol Microbiol	10.1099/ijsem.0.004374	2020	*
Phylogeny	Rhizobium wuzhouense sp. nov., isolated from roots of Oryza officinalis.	Yuan T, Liu L, Huang S, Taher AH, Tan Z, Wu G, Peng G	Int J Syst Evol Microbiol	10.1099/ijsem.0.002921	2018	*
Phylogeny	Rhizobium ipomoeae sp. nov., isolated from a water convolvulus field.	Sheu SY, Chen ZH, Young CC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.000875	2016	*

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 )

#43690

Shih-Yi Sheu, Zih-Han Chen, Chiu-Chung Young, Wen-Ming Chen: Rhizobium ipomoeae sp. nov., isolated from a water convolvulus field. IJSEM 66: 1633 - 1640 2016 ( DOI 10.1099/ijsem.0.000875 , PubMed 26739022 )

#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) .

#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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