Agrobacterium salinitolerans (LMG 29287, HAMBI 3646, YIC 5082)

Name: Agrobacterium salinitolerans (LMG 29287, HAMBI 3646, YIC 5082)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140485

Type strain

Culture col. no. LMG 29287 HAMBI 3646 YIC 5082

NCBI tax ID(s) 1183413

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Agrobacterium salinitolerans LMG 29287 is an aerobe, mesophilic, Gram-negative prokaryote that forms circular colonies and was isolated from surface-sterilized effective root nodules of S. cannabina.

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

Name and taxonomic classification

SI-ID 272883

LMG 29287

@ref 20215

Last LPSN update 2025-12-16 10:03:36

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Agrobacterium

Species Agrobacterium salinitolerans

Full scientific name Agrobacterium salinitolerans Yan et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
43242	negative	0.79-1.48 µm	0.41-0.5 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43242	2-3 mm	cream-white	circular	3 days	YMA

Culture and growth conditions

Culture medium

@ref	Name	Growth
43242	YMA

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
43242	positive	optimum	28	mesophilic
43242	positive	growth	20-37

Culture pH

@ref	Ability	Type	PH	PH range
43242	positive	optimum	8
43242	positive	growth	6-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

43242

Oxygen toleranceaerobe

Spore formation

43242

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43242	NaCl	positive	growth	0-5 %(w/v)
43242	NaCl	positive	optimum	3 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43242	62064 ChEBI	2,3-butanediol	-	carbon source
43242	30916 ChEBI	2-oxoglutarate	+	carbon source
43242	30089 ChEBI	acetate	+	carbon source
43242	8295 ChEBI	beta-hydroxybutyrate	+	carbon source
43242	16947 ChEBI	citrate	+	carbon source
43242	15570 ChEBI	D-alanine	+	carbon source
43242	15748 ChEBI	D-glucuronate	+	carbon source
43242	27605 ChEBI	D-psicose	+	carbon source
43242	17924 ChEBI	D-sorbitol	-	carbon source
43242	23652 ChEBI	dextrin	+	carbon source
43242	15740 ChEBI	formate	+	carbon source
43242	16865 ChEBI	gamma-aminobutyric acid	+	carbon source
43242	28087 ChEBI	glycogen	+	carbon source
43242	73804 ChEBI	glycyl L-aspartic acid	+	carbon source
43242	73784 ChEBI	glycyl-l-glutamate	-	carbon source
43242	21217 ChEBI	L-alaninamide	-	carbon source
43242	15971 ChEBI	L-histidine	+	carbon source
43242	18183 ChEBI	L-pyroglutamic acid	+	carbon source
43242	17115 ChEBI	L-serine	-	carbon source
43242	16857 ChEBI	L-threonine	+	carbon source
43242	51850 ChEBI	methyl pyruvate	+	carbon source
43242	75146 ChEBI	monomethyl succinate	+	carbon source
43242	28037 ChEBI	N-acetylgalactosamine	+	carbon source
43242	17632 ChEBI	nitrate	-	reduction
43242	28017 ChEBI	starch	+	hydrolysis
43242	143136 ChEBI	succinamate	+	carbon source
43242	53426 ChEBI	tween 80	+	carbon source
43242	16199 ChEBI	urea	+	hydrolysis
43242	16704 ChEBI	uridine	-	carbon source
43242	27248 ChEBI	urocanic acid	+	carbon source

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
43242	28971	ampicillin	300 µg/mL
43242	28971	ampicillin		100 µg/mL
43242	17698	chloramphenicol	300 µg/mL
43242	17698	chloramphenicol		100 µg/mL
43242	48923	erythromycin		300 µg/mL
43242	6104	kanamycin	300 µg/mL
43242	6104	kanamycin		100 µg/mL
43242	7507	neomycin	50 µg/mL
43242	7507	neomycin		5 µg/mL
43242	17076	streptomycin	300 µg/mL
43242	17076	streptomycin		100 µg/mL

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43242	15688 ChEBI	acetoin

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
43242	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
43242	catalase	+	1.11.1.6
43242	cytochrome oxidase	+	1.9.3.1

Fatty acid profile

Metadata FA analysis

@ref

43242

Fatty acid	Percentage
C16:0	9.5
C16:0 3OH	4.93
C17:0 cyclo	4.01
C18:0	1.84
C13:1 AT12-13	1.53
C14:0	1.08
C18:0 3OH	0.3
C12:0	0.18
C17:0	0.15
C17:0 anteiso	0.15
C17:0 iso 3OH	0.14
C17:1ω8c	0.11

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Shrub (Scrub)
#Host Body-Site	#Plant	#Root nodule
#Host Body-Site	#Plant	#Sterilized plant part

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature
43242	surface-sterilized effective root nodules of S. cannabina	Rudong Country, Jiangsu Province	China	CHN	Asia	YMA	3 days	28

Taxonmaps

69479

Global distribution of 16S sequence KP142169 (>99% sequence identity) for Rhizobiaceae from Microbeatlas

Aquatic Samples	386
Soil Samples	235
Animal Samples	2243
Plant Samples	147
Total Samples	3011

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
124043	ASM200822v1 assembly for Agrobacterium salinitolerans YIC 5082	scaffold	GCA_002008225	2858630679	1183413	71.12

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
43242	Agrobacterium salinitolerans strain YIC 5082 16S ribosomal RNA gene, partial sequence	KP142169	1341	1923828
124043	Agrobacterium salinitolerans strain YIC 5082 16S ribosomal RNA gene, partial sequence.	OQ875713	389	1183413
124043	Agrobacterium salinitolerans strain YIC 5082 16S ribosomal RNA gene, partial sequence.	OQ875743	1341	1183413

GC content

@ref	GC-content (mol%)	Method
43242	59.3	sequence analysis

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Pathogenicity	Dynamic multi-omics mechanisms underpinning retinol tolerance: stage-specific reconstruction of skin barrier function and host-microbiome metabolic interactions.	Huang Y, Zhou Q, Gui M, Guo D, Cheng J, Ma W, Shu P, Liu X.	Front Microbiol	10.3389/fmicb.2025.1668712	2025
Genetics	Draft genome sequence of Agrobacterium pusense strain CMT1: A promising growth-promoting bacterium isolated from nodules of soybean (Glycine max L. Merrill) crops for the One Health approach in Paraguay.	Samudio Oggero A, Valdez Borda M, Felix Pablos CM, Leguizamon G, Morinigo FM, Gonzalez Caballero V, Farias A, Nakayama H, de Los Santos Villalobos S.	Curr Res Microb Sci	10.1016/j.crmicr.2024.100259	2024
Genetics	Genome Sequence of the Agrobacterium salinitolerans DG3-1 Isolated from Cotton Roots.	Hao H, Wang Z, Gou C, Sha S, Yan C, Niu D, Wang L, Feng H.	Mol Plant Microbe Interact	10.1094/mpmi-06-21-0154-a	2021
Pathogenicity	Network pharmacological prediction of chemical constituents and endophyte metabolites of medicinal plant Shengli grass.	Zhao L, Huang X, Xu Y, Xi L, Song W, Xing X, Liu M, Li M, Hou Y.	Sci Rep	10.1038/s41598-025-20961-3	2025
	Diversity and functional assessment of indigenous culturable bacteria inhabiting fine-flavor cacao rhizosphere: Uncovering antagonistic potential against Moniliophthora roreri.	Crisostomo-Panuera JS, Nieva ASDV, Ix-Balam MA, Diaz-Valderrama JR, Alviarez-Gutierrez E, Oliva-Cruz SM, Cumpa-Velasquez LM.	Heliyon	10.1016/j.heliyon.2024.e28453	2024
	Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach.	Hiergeist A, Ruelle J, Emler S, Gessner A.	PLoS One	10.1371/journal.pone.0280870	2023
	An aerotaxis receptor influences invasion of Agrobacterium tumefaciens into its host.	Huang Z, Zou J, Guo M, Zhang G, Gao J, Zhao H, Yan F, Niu Y, Wang GL.	PeerJ	10.7717/peerj.16898	2024
	Back to the Roots: Agrobacterium-Specific Phages Show Potential to Disinfect Nutrient Solution from Hydroponic Greenhouses.	Fortuna KJ, Holtappels D, Venneman J, Baeyen S, Vallino M, Verwilt P, Rediers H, De Coninck B, Maes M, Van Vaerenbergh J, Lavigne R, Wagemans J.	Appl Environ Microbiol	10.1128/aem.00215-23	2023
	Divergent endophytic viromes and phage genome repertoires among banana (Musa) species.	Aghdam SA, Lahowetz RM, Brown AMV.	Front Microbiol	10.3389/fmicb.2023.1127606	2023
Genetics	Plasmids Related to the Symbiotic Nitrogen Fixation Are Not Only Cooperated Functionally but Also May Have Evolved over a Time Span in Family Rhizobiaceae.	Yang LL, Jiang Z, Li Y, Wang ET, Zhi XY.	Genome Biol Evol	10.1093/gbe/evaa152	2020
Metabolism	Detection of antibiotics synthetized in microfluidic picolitre-droplets by various actinobacteria.	Mahler L, Wink K, Beulig RJ, Scherlach K, Tovar M, Zang E, Martin K, Hertweck C, Belder D, Roth M.	Sci Rep	10.1038/s41598-018-31263-2	2018
Genetics	Comparative Genomics of Novel Agrobacterium G3 Strains Isolated From the International Space Station and Description of Agrobacterium tomkonis sp. nov.	Singh NK, Lavire C, Nesme J, Vial L, Nesme X, Mason CE, Lassalle F, Venkateswaran K.	Front Microbiol	10.3389/fmicb.2021.765943	2021
Phylogeny	Agrobacterium salinitolerans sp. nov., a saline-alkaline-tolerant bacterium isolated from root nodule of Sesbania cannabina.	Yan J, Li Y, Yan H, Chen WF, Zhang X, Wang ET, Han XZ, Xie ZH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001885	2017

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 )
#43242	Jun Yan, Yan Li, Hui Yan, Wen Feng Chen, Xiaoxia Zhang, En Tao Wang, Xiao Zeng Han, Zhi Hong Xie: Agrobacterium salinitolerans sp. nov., a saline-alkaline-tolerant bacterium isolated from root nodule of Sesbania cannabina. IJSEM 67: 1906 - 1911 2017 ( DOI 10.1099/ijsem.0.001885 , PubMed 28629499 )
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Agrobacterium salinitolerans (LMG 29287, HAMBI 3646, YIC 5082)

Name and taxonomic classification