Ensifer fredii (DSM 5851, ATCC 35423, LMG 6217)

Name: Ensifer fredii (DSM 5851, ATCC 35423, LMG 6217)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13548

Type strain

Culture col. no. DSM 5851 ATCC 35423 LMG 6217 USDA 205 CCUG 27877 12 more

NCBI tax ID(s) 380

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- Wen-Xin Chen <- Yang Su-Scheng <- H.H. Keyser JCM <-- IAM 13625 <-- USDA 205. CIP <- 2002, P. de Lajudie, Montpellier, France: strain ORS 669T <- LMG <- 1984, B. Jarvis, Rhizobium sp.

Links

Ensifer fredii DSM 5851 is a Gram-negative, motile, rod-shaped bacterium that was isolated from soybean nodules.

Gram-negative motile rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 4760

LMG 6217,ATCC 35423,NCIB 12104,CCUG 27877,NCIMB 12104,IAM13625,IFO 14780,CECT 4369,CCRC 13525,HAMBI 2075,ICMP 11139,NRRL B-14594,NBRC 14780,NRRL B-14241,BCRC 13525,CCT 4161,ICMP 13647,KACC 10641,JCM 20967,CFBP 6722,CIP 107333,NCPPB 4145,DSM 5851

@ref 20215

Last LPSN update 2026-05-29 08:28:04

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Ensifer

Species Ensifer fredii

Full scientific name Ensifer fredii (Scholla and Elkan 1984) Young 2003

Synonyms (5)

Sinorhizobium fredii
Rhizobium fredii
Sinorhizobium xinjiangense
Sinorhizobium xinjiangensis
Ensifer xinjiangensis

BacDive ID	Other strains from **Ensifer fredii** (4)	Type strain
13549	E. fredii R x 42, DSM 5852, ATCC 49357, CCBAU 110, ...
13550	E. fredii DSM 5924, USDA 194
163040	E. fredii JCM 20968, IAM 13626, LMG 6219, USDA 208
163041	E. fredii JCM 20969, IAM 13627, LMG 6216, LMG 8317, ...

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125438	negative		98.833
125439	negative		97.244
119450	negative	rod-shaped

Colony morphology

119450

Hemolysis ability0

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2339	RHIZOBIUM MEDIUM (DSMZ Medium 98)	Medium recipe at MediaDive	Name: RHIZOBIUM MEDIUM (DSMZ Medium 98) Composition: air-dried garden soil 80.0 g/l Agar 15.0 g/l Mannitol 10.0 g/l Yeast extract 1.0 g/l Na2CO3 0.2 g/l Distilled water
38202	MEDIUM 296 - for Rhizobium		Distilled water make up to (800.000 ml);Agar (15.000 g);Yeast extract (1.000 g);Mannitol (10.000 g);Earth extract - M0541 (200.000 ml)
119450	CIP Medium 296	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
2339	positive	growth	28
38202	positive	growth	30
67770	positive	growth	25
119450	positive	growth	25-30
119450	negative	growth	10
119450	negative	growth	37
119450	negative	growth	41
119450	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.848

Spore formation

@ref	Spore formation	Confidence
125439		99.371

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119450	NaCl	positive	growth	0 %
119450	NaCl		growth	2 %
119450	NaCl		growth	4 %
119450	NaCl		growth	6 %
119450	NaCl		growth	8 %
119450	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
119450	16947 ChEBI	citrate	-	carbon source
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
119450	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
119450	606565 ChEBI	hippurate	-	hydrolysis
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
119450	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
119450	16301 ChEBI	nitrite	+	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
119450	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
119450	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test	Voges-proskauer-test	Methylred-test
119450	15688 ChEBI	acetoin		-
119450	17234 ChEBI	glucose			-
68369	35581 ChEBI	indole	-			from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119450	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
119450	amylase	-
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	+	3.2.1.23	from API zym
119450	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119450	caseinase	-	3.4.21.50
119450	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
119450	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119450	gamma-glutamyltransferase	-	2.3.2.2
119450	gelatinase	-
68369	gelatinase	-		from API 20NE
119450	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119450	lipase	-
68382	lipase (C 14)	-		from API zym
119450	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119450	ornithine decarboxylase	-	4.1.1.17
119450	oxidase	+
119450	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
119450	tryptophan deaminase	-
119450	tween esterase	-
119450	urease	+	3.5.1.5
68369	urease	+	3.5.1.5	from API 20NE
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119450	-	+	+	+	-	+	-	-	+	-	+	+	-	+	-	+	+	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
2339	-	-	-	-	+	+	-	+	+/-	-	+/-	+	-	+	-	-	-	+	-	-	+
2339	-	-	-	-	+	+	-	+	+	+	+	+	+	+	+/-	-	+	+	-	-	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
119450	not determinedn.d.	+	+	+	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	+	-	+	+	+	+	-	+	-	-	-	-	+	+	+	-	-	+	+	-	-	+	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	+	-	-	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	+	+	+	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
2339	soybean nodules
48991	Soy bean,Glycine max,root nodule	Honan	China	CHN	Asia
67770	Root nodule of soybean	Honan	China	CHN	Asia
119450	Plant, Glycine max, soybean root nodule	Honan	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence NR_036957 (>99% sequence identity) for Rhizobiaceae from Microbeatlas

Aquatic Samples	1562
Soil Samples	5353
Animal Samples	1094
Plant Samples	1478
Total Samples	9487

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2339	1	Risk group (German classification) According to TRBA 466
119450	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score	IMG accession
124043	ASM3016079v1 assembly for Sinorhizobium fredii NBRC 14780	scaffold	GCA_030160795	380.66	380	38.8
124043	ASM146169v1 assembly for Sinorhizobium fredii USDA 205	contig	GCA_001461695		1230631	29.64	2728369612
67770	ASM653960v1 assembly for Sinorhizobium fredii NBRC 14780	contig	GCA_006539605	380.55	380	17.65

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Sinorhizobium fredii gene for 16S rRNA, complete sequence, type strain: ATCC 35423	D14516	1481	380
20218	Sinorhizobium fredii gene for 16S rRNA, strain: IAM 13625	D12792	1438	380
20218	Sinorhizobium fredii strain LMG 6217 16S ribosomal RNA gene, partial sequence; internal transcribed spacer, complete sequence; and 23S ribosomal RNA, partial sequence	AF345282	1060	380
20218	Sinorhizobium fredii partial 16S rRNA gene, strain LMG 6217	X67231	1437	380
20218	Sinorhizobium fredii gene for 16S rRNA, partial sequence, strain: NBRC 14780	AB680661	1410	380
20218	Sinorhizobium fredii gene for 16S rRNA, partial sequence, strain: USDA 205	AB433353	1407	380
20218	Sinorhizobium fredii strain USDA 205 16S-23S ribosomal RNA intergenic spacer region	AF284451	1142	380
20218	Sinorhizobium fredii strain USDA205 16S ribosomal RNA gene, partial sequence	AY260149	1421	380
20218	Sinorhizobium fredii strain USDA205 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	HQ143405	821	380
20218	Rhizobium fredii 16S ribosomal RNA gene, partial	M74163	260	380
2339	Sinorhizobium fredii strain USDA 205 16S ribosomal RNA, partial sequence	NR_036957	1437	380

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3016079v1 assembly for Sinorhizobium fredii NBRC 14780
NCBI: GCA_030160795

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.85	no
125439	gram_stain	BacteriaNetⓘ	negative	97.24	no
125439	spore_formation	BacteriaNetⓘ	no	99.37	no
125439	motility	BacteriaNetⓘ	yes	47.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sinorhizobium fredii strain NBRC 14780
PATRIC: 380.55

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.83	no
125438	anaerobic	anaerobicⓘ	no	95.40	no
125438	spore-forming	spore-formingⓘ	no	86.27	no
125438	aerobic	aerobicⓘ	yes	87.06	no
125438	thermophilic	thermophileⓘ	no	99.42	no
125438	flagellated	motile2+ⓘ	yes	72.31	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Catabolism of 1,5-anhydro-D-fructose in Sinorhizobium morelense S-30.7.5: discovery, characterization, and overexpression of a new 1,5-anhydro-D-fructose reductase and its application in sugar analysis and rare sugar synthesis.	Kuhn A, Yu S, Giffhorn F.	Appl Environ Microbiol	10.1128/aem.72.2.1248-1257.2006	2006
	Mycorrhizae Enhance Soybean Plant Growth and Aluminum Stress Tolerance by Shaping the Microbiome Assembly in an Acidic Soil.	Wen Z, Yang M, Han H, Fazal A, Liao Y, Ren R, Yin T, Qi J, Sun S, Lu G, Hu S, Yang Y.	Microbiol Spectr	10.1128/spectrum.03310-22	2023
	Genetic diversity of indigenous common bean (Phaseolus vulgaris L.) rhizobia from the state of Minas Gerais, Brazil.	Torres AR, Cursino L, Muro-Abad JI, Gomes EA, de Araujo EF, Hungria M, Cassini ST.	Braz J Microbiol	10.1590/s1517-838220090004000016	2009
Genetics	Microbial Alliances: Unveiling the Effects of a Bacterial and Fungal Cross-Kingdom SynCom on Bacterial Dynamics, Rhizosphere Metabolites, and Soybean Resilience in Acidic Soils.	Wen Z, Yang M, Lu G, Han M, Song Y, Sun Y, Tu Q, Yin T, Niu K, Sun S, Qi J, Fazal A, Yang Y.	J Agric Food Chem	10.1021/acs.jafc.4c12416	2025
	Insights into the production of erythritol by strains of Limosilactobacillus fermentum of sourdough origin.	Gonzalez-Alonso V, Verce M, Pradal I, Leroy F, De Vuyst L.	Appl Environ Microbiol	10.1128/aem.01565-25	2025
Genetics	Regulation of Root Nodule Symbiosis by Soybean Rj Genotypes and Rhizobial Effectors.	Fukunaga S, Ratu STN, Okazaki S.	Microbes Environ	10.1264/jsme2.me25027	2025
Phylogeny	Cultivation of Genetically Modified Soybeans Did Not Alter the Overall Structure of Rhizosphere Soil Microbial Communities.	Shen W, Liu L, Fang Z, Zhang L, Ren Z, Yu Q, Yin X, Liu B.	Plants (Basel)	10.3390/plants14030457	2025
Phylogeny	Ensifer fredii symbiovar vachelliae nodulates endemic Vachellia gummifera in semiarid Moroccan areas.	Bouhnik O, ElFaik S, Alami S, Talbi C, Lamin H, Abdelmoumen H, Tortosa Munoz G, J Bedmar E, Missbah El Idrissi M.	Syst Appl Microbiol	10.1016/j.syapm.2019.06.004	2019
	Nodulation Is Maintained and Salinity Tolerance Enhanced in Two Soybean Cultivars Inoculated With Sinorhizobium fredii Under Brackish Water.	Perez-Sepulveda M, Jones AP, Higuita-Aguirre MI, Holdstock A, Kafle A, Cardoso AA, Vann R, Mullen MD, Garcia K.	Physiol Plant	10.1111/ppl.70570	2025
Pathogenicity	Guidelines for the description of rhizobial symbiovars.	Martinez-Romero E, Peix A, Hungria M, Mousavi SA, Martinez-Romero J, Young P.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006373	2024
	Covalent fragment screening to inhibit the E3 ligase activity of bacterial NEL enzymes SspH1 and SspH2.	Kennedy CR, McPhie KA, Vuorinen A, Dudley-Fraser J, Esposito D, Maslen S, McCarthy WJ, Pettinger J, Skehel JM, Bush J, House D, Rittinger K.	RSC Chem Biol	10.1039/d5cb00177c	2025
	Secretory molecules from secretion systems fine-tune the host-beneficial bacteria (PGPRs) interaction.	Gupta G, Chauhan PS, Jha PN, Verma RK, Singh S, Yadav VK, Sahoo DK, Patel A.	Front Microbiol	10.3389/fmicb.2024.1355750	2024
	A beta-1,2-glucan-associated glycoside hydrolase family 1 beta-glucosidase from Streptomyces griseus.	Kumakura H, Motouchi S, Kobayashi K, Inoue M, Kariuda N, Nakai H, Nakajima M.	Protein Sci	10.1002/pro.70255	2025
Metabolism	Identification of Soybean Genes Whose Expression is Affected by the Ensifer fredii HH103 Effector Protein NopP.	Wang J, Wang J, Liu C, Ma C, Li C, Zhang Y, Qi Z, Zhu R, Shi Y, Zou J, Li Q, Zhu J, Wen Y, Sun Z, Liu H, Jiang H, Yin Z, Hu Z, Chen Q, Wu X, Xin D.	Int J Mol Sci	10.3390/ijms19113438	2018
	Rhizobial biogeography and inoculation application to soybean in four regions across China.	Yang SH, Chen WH, Wang ET, Chen WF, Yan J, Han XZ, Tian CF, Sui XH, Singh RP, Jiang GM, Chen WX.	J Appl Microbiol	10.1111/jam.13897	2018
	A novel symbiovar (aegeanense) of the genus Ensifer nodulates Vigna unguiculata	Tampakaki AP, Fotiadis CT, Ntatsi G, Savvas D.	Journal of the Science of Food and Agriculture.		2017
	Genetic Characterization and Symbiotic Performance of Soybean Rhizobia Under Cold and Water-Deficient Conditions in Poland.	Watanabe R, Artigas Ramirez MD, Agake SI, Bellingrath-Kimura SD, Lewandowska S, Onishi Y, Nishikawa Y, Takeyama H, Yasuda M, Ohkama-Ohtsu N.	Plants (Basel)	10.3390/plants14121786	2025
Enzymology	Lipo-Chitooligosaccharides (LCOs) as Elicitors of the Enzymatic Activities Related to ROS Scavenging to Alleviate Oxidative Stress Generated in Tomato Plants under Stress by UV-B Radiation.	Lucas JA, Garcia-Villaraco A, Ramos-Solano B, Akdi K, Gutierrez-Manero FJ.	Plants (Basel)	10.3390/plants11091246	2022
	The host niches of soybean rather than genetic modification or glyphosate application drive the assembly of root-associated microbial communities.	Yang M, Luo F, Song Y, Ma S, Ma Y, Fazal A, Yin T, Lu G, Sun S, Qi J, Wen Z, Li Y, Yang Y.	Microb Biotechnol	10.1111/1751-7915.14164	2022
Phylogeny	A novel symbiovar (aegeanense) of the genus Ensifer nodulates Vigna unguiculata.	Tampakaki AP, Fotiadis CT, Ntatsi G, Savvas D.	J Sci Food Agric	10.1002/jsfa.8281	2017
	The costs and benefits of symbiotic interactions: variable effects of rhizobia and arbuscular mycorrhizae on Vigna radiata accessions.	Chien CC, Tien SY, Yang SY, Lee CR.	BMC Plant Biol	10.1186/s12870-024-05488-5	2024
	Symbiotic matching, taxonomic position, and field assessment of symbiotically efficient rhizobia isolated from soybean root nodules in Sichuan, China	Chen YX, Zhou T, Penttinen P, Zou L, Wang K, Cui YQ, Heng NN, Xu KW.	Biol Fertil Soils	10.1007/s00374-015-1019-y	2015
Phylogeny	Phylogenetic Diversity of Ammopiptanthus Rhizobia and Distribution of Rhizobia Associated with Ammopiptanthus mongolicus in Diverse Regions of Northwest China.	Zhao L, Wang X, Huo H, Yuan G, Sun Y, Zhang D, Cao Y, Xu L, Wei G.	Microb Ecol	10.1007/s00248-016-0759-z	2016
Pathogenicity	Impact of a G2-EPSPS & GAT Dual Transgenic Glyphosate-Resistant Soybean Line on the Soil Microbial Community under Field Conditions Affected by Glyphosate Application.	Yang M, Wen Z, Fazal A, Hua X, Xu X, Yin T, Qi J, Yang R, Lu G, Hong Z, Yang Y.	Microbes Environ	10.1264/jsme2.me20056	2020
Phylogeny	Distribution and diversity of rhizobia associated with wild soybean (Glycine soja Sieb. & Zucc.) in Northwest China.	Zhao L, Fan M, Zhang D, Yang R, Zhang F, Xu L, Wei X, Shen Y, Wei G.	Syst Appl Microbiol	10.1016/j.syapm.2014.05.011	2014
Phylogeny	Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping.	Fagorzi C, Ilie A, Decorosi F, Cangioli L, Viti C, Mengoni A, diCenzo GC.	Genome Biol Evol	10.1093/gbe/evaa221	2020
	Bradyrhizobium ottawaense efficiently reduces nitrous oxide through high nosZ gene expression.	Wasai-Hara S, Itakura M, Fernandes Siqueira A, Takemoto D, Sugawara M, Mitsui H, Sato S, Inagaki N, Yamazaki T, Imaizumi-Anraku H, Shimoda Y, Minamisawa K.	Sci Rep	10.1038/s41598-023-46019-w	2023
Genetics	The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations.	Dang X, Xie Z, Liu W, Sun Y, Liu X, Zhu Y, Staehelin C.	BMC Genomics	10.1186/s12864-019-6004-7	2019
Phylogeny	Nodule and Root Zone Microbiota of Salt-Tolerant Wild Soybean in Coastal Sand and Saline-Alkali Soil.	Yang Y, Liu L, Singh RP, Meng C, Ma S, Jing C, Li Y, Zhang C.	Front Microbiol	10.3389/fmicb.2020.523142	2020
Phylogeny	The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling.	Zhang T, Li H, Ma S, Cao J, Liao H, Huang Q, Chen W.	Appl Environ Microbiol	10.1128/aem.00605-23	2023
	Soil biochar amendment affects the diversity of nosZ transcripts: Implications for N₂O formation.	Harter J, El-Hadidi M, El-Hadidi M, Huson DH, Kappler A, Behrens S.	Sci Rep	10.1038/s41598-017-03282-y	2017
Phylogeny	Characterization of root-nodulating bacteria associated to Prosopis farcta growing in the arid regions of Tunisia.	Fterich A, Mahdhi M, Caviedes MA, Pajuelo E, Rivas R, Rodriguez-Llorente ID, Mars M.	Arch Microbiol	10.1007/s00203-011-0683-z	2011
Phylogeny	Genetic Characterization of Soybean Rhizobia Isolated from Different Ecological Zones in North-Eastern Afghanistan.	Habibi S, Ayubi AG, Ohkama-Ohtsu N, Sekimoto H, Yokoyama T.	Microbes Environ	10.1264/jsme2.me16119	2017
Metabolism	The Sinorhizobium (Ensifer) fredii HH103 Nodulation Outer Protein NopI Is a Determinant for Efficient Nodulation of Soybean and Cowpea Plants.	Jimenez-Guerrero I, Perez-Montano F, Medina C, Ollero FJ, Lopez-Baena FJ.	Appl Environ Microbiol	10.1128/aem.02770-16	2017
Phylogeny	Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium).	Martens M, Dawyndt P, Coopman R, Gillis M, De Vos P, Willems A.	Int J Syst Evol Microbiol	10.1099/ijs.0.65392-0	2008
Metabolism	NopC Is a Rhizobium-Specific Type 3 Secretion System Effector Secreted by Sinorhizobium (Ensifer) fredii HH103.	Jimenez-Guerrero I, Perez-Montano F, Medina C, Ollero FJ, Lopez-Baena FJ.	PLoS One	10.1371/journal.pone.0142866	2015
	Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation.	Kuzmanovic N, Fagorzi C, Mengoni A, Lassalle F, diCenzo GC.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005243	2022
	Factors affecting the attachment of rhizospheric bacteria to bean and soybean roots.	Albareda M, Dardanelli MS, Sousa C, Megias M, Temprano F, Rodriguez-Navarro DN.	FEMS Microbiol Lett	10.1111/j.1574-6968.2006.00244.x	2006
Genetics	Patterns in the Microbial Community of Salt-Tolerant Plants and the Functional Genes Associated with Salt Stress Alleviation.	Zheng Y, Xu Z, Liu H, Liu Y, Zhou Y, Meng C, Ma S, Xie Z, Li Y, Zhang CS.	Microbiol Spectr	10.1128/spectrum.00767-21	2021
	The Contribution of PGPR in Salt Stress Tolerance in Crops: Unravelling the Molecular Mechanisms of Cross-Talk between Plant and Bacteria.	Giannelli G, Potestio S, Visioli G.	Plants (Basel)	10.3390/plants12112197	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
Genetics	Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts.	Le Quere A, Tak N, Gehlot HS, Lavire C, Meyer T, Chapulliot D, Rathi S, Sakrouhi I, Rocha G, Rohmer M, Severac D, Filali-Maltouf A, Munive JA.	BMC Genomics	10.1186/s12864-016-3447-y	2017
	High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris.	Mhamdi R, Ardley J, Tian R, Seshadri R, Reddy TB, Pati A, Woyke T, Markowitz V, Ivanova N, Kyrpides N, Reeve W.	Stand Genomic Sci	10.1186/s40793-015-0005-1	2015
Phylogeny	The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensifer adhaerens Casida 1982. Is the combination "Sinorhizobium adhaerens" (Casida 1982) Willems et al. 2003 legitimate? Request for an Opinion.	Young JM.	Int J Syst Evol Microbiol	10.1099/ijs.0.02665-0	2003
	Transcriptomic and photosynthetic responses to grafting of the Nod1 gene in nodulated and non-nodulated soybeans.	He Q, Xiang S, Wang W, Shu Y, Li Z, Wang S, Chen L, Yang X, Zhao T.	G3 (Bethesda)	10.1093/g3journal/jkab209	2021
Phenotype	Multiple Metabolic Phenotypes as Screening Criteria Are Correlated With the Plant Growth-Promoting Ability of Rhizobacterial Isolates.	Shi P, Zhang J, Li X, Zhou L, Luo H, Wang L, Zhang Y, Chou M, Wei G.	Front Microbiol	10.3389/fmicb.2021.747982	2021
	A Stringent-Response-Defective Bradyrhizobium diazoefficiens Strain Does Not Activate the Type 3 Secretion System, Elicits an Early Plant Defense Response, and Circumvents NH₄NO₃-Induced Inhibition of Nodulation.	Perez-Gimenez J, Iturralde ET, Torres Tejerizo G, Quelas JI, Krol E, Borassi C, Becker A, Estevez JM, Lodeiro AR.	Appl Environ Microbiol	10.1128/aem.02989-20	2021
	High-quality draft genome sequence of Rhizobium mesoamericanum strain STM6155, a Mimosa pudica microsymbiont from New Caledonia.	Klonowska A, Lopez-Lopez A, Moulin L, Ardley J, Gollagher M, Marinova D, Tian R, Huntemann M, Reddy TB, Varghese N, Woyke T, Markowitz V, Ivanova N, Seshadri R, Baeshen MN, Baeshen NA, Kyrpides N, Reeve W.	Stand Genomic Sci	10.1186/s40793-016-0212-4	2017
	Symbiotic incompatibility between soybean and Bradyrhizobium arises from one amino acid determinant in soybean Rj2 protein.	Sugawara M, Umehara Y, Kaga A, Hayashi M, Ishimoto M, Sato S, Mitsui H, Minamisawa K.	PLoS One	10.1371/journal.pone.0222469	2019
	NopD of Bradyrhizobium sp. XS1150 Possesses SUMO Protease Activity.	Xiang QW, Bai J, Cai J, Huang QY, Wang Y, Liang Y, Zhong Z, Wagner C, Xie ZP, Staehelin C.	Front Microbiol	10.3389/fmicb.2020.00386	2020
	Rhizobia use a pathogenic-like effector to hijack leguminous nodulation signalling.	Ratu STN, Teulet A, Miwa H, Masuda S, Nguyen HP, Yasuda M, Sato S, Kaneko T, Hayashi M, Giraud E, Okazaki S.	Sci Rep	10.1038/s41598-021-81598-6	2021
	Phylogeny of Symbiotic Genes and the Symbiotic Properties of Rhizobia Specific to Astragalus glycyphyllos L.	Gnat S, Malek W, Olenska E, Wdowiak-Wrobel S, Kalita M, Lotocka B, Wojcik M.	PLoS One	10.1371/journal.pone.0141504	2015
Genetics	The complete replicons of 16 Ensifer meliloti strains offer insights into intra- and inter-replicon gene transfer, transposon-associated loci, and repeat elements.	Nelson M, Guhlin J, Epstein B, Tiffin P, Sadowsky MJ.	Microb Genom	10.1099/mgen.0.000174	2018
Metabolism	Discovery of Novel Plant Interaction Determinants from the Genomes of 163 Root Nodule Bacteria.	Seshadri R, Reeve WG, Ardley JK, Tennessen K, Woyke T, Kyrpides NC, Ivanova NN.	Sci Rep	10.1038/srep16825	2015
	High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India.	Gehlot HS, Ardley J, Tak N, Tian R, Poonar N, Meghwal RR, Rathi S, Tiwari R, Adnawani W, Seshadri R, Reddy TB, Pati A, Woyke T, Pillay M, Markowitz V, Baeshen MN, Al-Hejin AM, Ivanova N, Kyrpides N, Reeve W.	Stand Genomic Sci	10.1186/s40793-016-0157-7	2016
	Deciphering the Symbiotic Significance of Quorum Sensing Systems of Sinorhizobium fredii HH103.	Acosta-Jurado S, Alias-Villegas C, Almozara A, Espuny MR, Vinardell JM, Perez-Montano F.	Microorganisms	10.3390/microorganisms8010068	2020
Metabolism	Bacterial Molecular Signals in the Sinorhizobium fredii-Soybean Symbiosis.	Lopez-Baena FJ, Ruiz-Sainz JE, Rodriguez-Carvajal MA, Vinardell JM.	Int J Mol Sci	10.3390/ijms17050755	2016
Transcriptome	Non-Additive Transcriptomic Responses to Inoculation with Rhizobia in a Young Allopolyploid Compared with Its Diploid Progenitors.	Powell AF, Doyle JJ.	Genes (Basel)	10.3390/genes8120357	2017
Pathogenicity	The Effect of Root Exudate 7,4'-Dihydroxyflavone and Naringenin on Soil Bacterial Community Structure.	Szoboszlay M, White-Monsant A, Moe LA.	PLoS One	10.1371/journal.pone.0146555	2016
Phylogeny	Burkholderia and Paraburkholderia are Predominant Soybean Rhizobial Genera in Venezuelan Soils in Different Climatic and Topographical Regions.	Ramirez MDA, Espana M, Aguirre C, Kojima K, Ohkama-Ohtsu N, Sekimoto H, Yokoyama T.	Microbes Environ	10.1264/jsme2.me18076	2019
Phylogeny	Microsymbionts of Phaseolus vulgaris in acid and alkaline soils of Mexico.	Verastegui-Valdes MM, Zhang YJ, Rivera-Orduna FN, Cheng HP, Sui XH, Wang ET.	Syst Appl Microbiol	10.1016/j.syapm.2014.08.005	2014
	Mutualistic co-evolution of type III effector genes in Sinorhizobium fredii and Bradyrhizobium japonicum.	Kimbrel JA, Thomas WJ, Jiang Y, Creason AL, Thireault CA, Sachs JL, Chang JH.	PLoS Pathog	10.1371/journal.ppat.1003204	2013
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
	Promotion of Nitrogen Fixation of Diverse Heterotrophs by Solid-Phase Humin.	Dey S, Kasai T, Katayama A.	Front Microbiol	10.3389/fmicb.2022.853411	2022
	The Soybean Rfg1 Gene Restricts Nodulation by Sinorhizobium fredii USDA193.	Fan Y, Liu J, Lyu S, Wang Q, Yang S, Zhu H	Front Plant Sci	10.3389/fpls.2017.01548	2017
	RNA-Seq Analysis of Differential Gene Expression Responding to Different Rhizobium Strains in Soybean (Glycine max) Roots.	Yuan S, Li R, Chen S, Chen H, Zhang C, Chen L, Hao Q, Shan Z, Yang Z, Qiu D, Zhang X, Zhou X	Front Plant Sci	10.3389/fpls.2016.00721	2016
Phylogeny	[A sinorhizobium fredll strain that effectively nodulate Medicago sativa].	Zhang H, Zhang H, Li X, Yang S	Wei Sheng Wu Xue Bao		2001
Pathogenicity	Production of cell-associated polysaccharides of Rhizobium fredii USDA205 is modulated by apigenin and host root extract.	Reuhs BL, Kim JS, Badgett A, Carlson RW	Mol Plant Microbe Interact	10.1094/mpmi-7-0240	1994
Genetics	Rhizobium fredii and Rhizobium meliloti produce 3-deoxy-D-manno-2-octulosonic acid-containing polysaccharides that are structurally analogous to group II K antigens (capsular polysaccharides) found in Escherichia coli.	Reuhs BL, Carlson RW, Kim JS	J Bacteriol	10.1128/jb.175.11.3570-3580.1993	1993
	Serological Relatedness of Rhizobium fredii to Other Rhizobia and to the Bradyrhizobia.	Sadowsky MJ, Bohlool BB, Keyser HH	Appl Environ Microbiol	10.1128/aem.53.8.1785-1789.1987	1987
	Growth of fast- and slow-growing rhizobia on ethanol.	Sadowsky MJ, Bohlool BB	Appl Environ Microbiol	10.1128/aem.52.4.951-953.1986	1986
Phylogeny	Ensifer glycinis sp. nov., a rhizobial species associated with species of the genus Glycine.	Yan H, Yan J, Sui XH, Wang ET, Chen WX, Zhang XX, Chen WF.	Int J Syst Evol Microbiol	10.1099/ijsem.0.001120	2016
Phylogeny	Ensifer shofinae sp. nov., a novel rhizobial species isolated from root nodules of soybean (Glycine max).	Chen WH, Yang SH, Li ZH, Zhang XX, Sui XH, Wang ET, Chen WX, Chen WF.	Syst Appl Microbiol	10.1016/j.syapm.2017.01.002	2017
Phylogeny	Diversity and phenotypic analyses of salt- and heat-tolerant wild bean Phaseolus filiformis rhizobia native of a sand beach in Baja California and description of Ensifer aridi sp. nov.	Rocha G, Le Quere A, Medina A, Cuellar A, Contreras JL, Carreno R, Bustillos R, Munoz-Rojas J, Villegas MDC, Chaintreuil C, Dreyfus B, Munive JA.	Arch Microbiol	10.1007/s00203-019-01744-7	2020
Genetics	Draft genome sequence of type strain HBR26^T and description of Rhizobium aethiopicum sp. nov.	Aserse AA, Woyke T, Kyrpides NC, Whitman WB, Lindstrom K.	Stand Genomic Sci	10.1186/s40793-017-0220-z	2017
Phylogeny	Notoacmeibacter marinus gen. nov., sp. nov., isolated from the gut of a limpet and proposal of Notoacmeibacteraceae fam. nov. in the order Rhizobiales of the class Alphaproteobacteria.	Huang Z, Guo F, Lai Q, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.001951	2017

References

#2339	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5851
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#38202	; Curators of the CIP;
#48991	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 27877
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#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 .
#119450	Collection of Institut Pasteur ; Curators of the CIP; CIP 107333
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Ensifer fredii (DSM 5851, ATCC 35423, LMG 6217)

Name and taxonomic classification

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Cell morphology

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