Name: Mesorhizobium sediminum YIM M12096
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133222

Type strain:

Species: Mesorhizobium sediminum

Culture col. no.: YIM M12096, CCTCC AB 2014219, KCTC 42205, JCM 30310

Strain history: W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM M12096.

NCBI tax ID(s): 1849104 (species)

Section

Mesorhizobium sediminum YIM M12096 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from deep-sea sediment.

Gram-negative
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	*Phyllobacteriaceae*
	Genus	*Mesorhizobium*
	Species	**Mesorhizobium sediminum**
	Full Scientific Name (LPSN)	Mesorhizobium sediminum Yuan et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25044]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #25044]	Cell length	1.5-2.0 µm

[Ref.: #25044]	Cell width	0.3-0.6 µm

[Ref.: #25044]	Cell shape	rod-shaped

[Ref.: #25044]

Cultivation medium used

modified YIM #38 agar medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25044]

Culture medium

modified YIM #38 agar medium

[Ref.: #25044]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #25044]			growth	10-37 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #67770]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #25044]			growth	5.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25044]

Oxygen tolerance

aerobe

[Ref.: #25044]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.994

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25044]		NaCl		growth	0-7.0	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25044]	2-hydroxybutyrate ChEBI	-	carbon source
[Ref.: #25044]	acetate ChEBI	+	carbon source
[Ref.: #25044]	acetate ChEBI	+	respiration
[Ref.: #25044]	acetoacetate ChEBI	+	carbon source
[Ref.: #25044]	acetoacetate ChEBI	+	respiration
[Ref.: #25044]	alpha-lactose ChEBI	-	carbon source
[Ref.: #25044]	aztreonam ChEBI	-	carbon source
[Ref.: #25044]	bromosuccinate ChEBI	-	carbon source
[Ref.: #25044]	cellulose ChEBI	-	hydrolysis
[Ref.: #25044]	D-arabitol ChEBI	+	carbon source
[Ref.: #25044]	D-arabitol ChEBI	+	respiration
[Ref.: #25044]	D-fructose ChEBI	+	carbon source
[Ref.: #25044]	D-fructose ChEBI	+	respiration
[Ref.: #25044]	D-fucose ChEBI	+	carbon source
[Ref.: #25044]	D-fucose ChEBI	+	respiration
[Ref.: #25044]	D-mannitol ChEBI	+	builds acid from
[Ref.: #25044]	D-mannitol ChEBI	+	carbon source
[Ref.: #25044]	D-mannitol ChEBI	+	respiration
[Ref.: #25044]	D-serine ChEBI	-	carbon source
[Ref.: #25044]	D-sorbitol ChEBI	-	carbon source
[Ref.: #25044]	D-sorbitol ChEBI	-	respiration
[Ref.: #25044]	dextrin ChEBI	-	carbon source
[Ref.: #25044]	formate ChEBI	-	carbon source
[Ref.: #25044]	formate ChEBI	-	respiration
[Ref.: #25044]	fusidate ChEBI	-	carbon source
[Ref.: #25044]	galactarate ChEBI	-	carbon source
[Ref.: #25044]	gelatin ChEBI	-	respiration
[Ref.: #25044]	gelatin ChEBI	+	hydrolysis
[Ref.: #25044]	gentiobiose ChEBI	-	carbon source
[Ref.: #25044]	glucose ChEBI	-	fermentation
[Ref.: #25044]	L-alanine ChEBI	+	carbon source
[Ref.: #25044]	L-alanine ChEBI	+	respiration
[Ref.: #25044]	L-arginine ChEBI	-	respiration
[Ref.: #25044]	L-aspartate ChEBI	+	carbon source
[Ref.: #25044]	L-aspartate ChEBI	+	respiration
[Ref.: #25044]	L-malate ChEBI	+	carbon source
[Ref.: #25044]	L-malate ChEBI	+	respiration
[Ref.: #25044]	L-serine ChEBI	+	carbon source
[Ref.: #25044]	L-serine ChEBI	+	respiration
[Ref.: #25044]	melibiose ChEBI	-	carbon source
[Ref.: #25044]	myo-inositol ChEBI	-	respiration
[Ref.: #25044]	myo-inositol ChEBI	-	carbon source
[Ref.: #25044]	n-acetylneuraminate ChEBI	-	carbon source
[Ref.: #25044]	nitrate ChEBI	-	reduction
[Ref.: #25044]	raffinose ChEBI	-	carbon source
[Ref.: #25044]	raffinose ChEBI	-	respiration
[Ref.: #25044]	sodium bromate ChEBI	-	carbon source
[Ref.: #25044]	sodium butyrate ChEBI	-	carbon source
[Ref.: #25044]	sodium butyrate ChEBI	-	respiration
[Ref.: #25044]	stachyose ChEBI	-	carbon source
[Ref.: #25044]	starch ChEBI	-	hydrolysis
[Ref.: #25044]	trehalose ChEBI	-	carbon source
[Ref.: #25044]	tryptophan ChEBI	-	energy source
[Ref.: #25044]	turanose ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #25044]	amikacin ChEBI	yes	30	µg (disc)
[Ref.: #25044]	cefuroxime ChEBI	yes	30	µg (disc)
[Ref.: #25044]	chloramphenicol ChEBI	yes	30	µg (disc)
[Ref.: #25044]	ciprofloxacin ChEBI	yes	5	µg (disc)
[Ref.: #25044]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #25044]	oxacillin ChEBI				yes	1	µg (disc)
[Ref.: #25044]	piperacillin ChEBI	yes	100	µg (disc)
[Ref.: #25044]	polymyxin b ChEBI	yes	300	Unit (disc)
[Ref.: #25044]	tetracycline ChEBI	yes	30	µg (disc)

	Metabolite production	Metabolite	Production
[Ref.: #25044]		indole ChEBI	no

	Physiological tests	Metabolite	Methylred-test	Indole test
[Ref.: #25044]		glucose ChEBI	-
[Ref.: #25044]		indole ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #25044]	acid phosphatase	-	3.1.3.2
[Ref.: #25044]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25044]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25044]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25044]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25044]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25044]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25044]	beta-D-fucosidase	-	3.2.1.38
[Ref.: #25044]	beta-galactosidase	-	3.2.1.23
[Ref.: #25044]	beta-glucosidase	-	3.2.1.21
[Ref.: #25044]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25044]	catalase	+	1.11.1.6
[Ref.: #25044]	cystine arylamidase	+	3.4.11.3
[Ref.: #25044]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25044]	esterase lipase (C 8)	+
[Ref.: #25044]	leucine arylamidase	+	3.4.11.1
[Ref.: #25044]	lipase	-
[Ref.: #25044]	lipase (C 14)	-
[Ref.: #25044]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25044]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25044]	trypsin	+	3.4.21.4
[Ref.: #25044]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25044]	urease	-	3.5.1.5
[Ref.: #25044]	valine arylamidase	+
	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.: #25044]	Sample type/isolated from	deep-sea sediment
[Ref.: #25044]	Country	Indian Ocean
[Ref.: #25044]	Enrichment culture	modified YIM #38 agar medium
[Ref.: #25044]	Enrichment culture composition	g/ldistilled water unless otherwise stated: yeast extract, 4; glucose, 4; malt extract, 3; B-vitamin solution 1 ml (0.5 mg each of thiamine-HCl, riboflavin, niacin, pyridoxin, calcium pantothenate, inositol, p–aminobenzoic acid and 0.25 mg biotin); sea salt, 13; agar, 12; pH 7.2
[Ref.: #25044]	Enrichment culture duration	14 days
[Ref.: #25044]	Enrichment culture temperature	28 ̊C
[Ref.: #25044]	Isolation date	2013-07
[Ref.: #25044]	Isolation/enrichment procedure	serial dilution technique

[Ref.: #67770]	Sample type/isolated from	Deep-sea sediment collected from the Indian Ocean
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KX151664 (>99% sequence identity) for Mesorhizobium from Microbeatlas

Aquatic Samples	42
Soil Samples	23
Animal Samples	5
Plant Samples	11
Total Samples	81

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.: #25044]	16S rRNA	KX151664		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Mesorhizobium sediminum KCTC 42205	GCA_013240295	contig	GenBank	1849104 tax ID
[Ref.: #66792]	Mesorhizobium sediminum strain KCTC 42205	1849104.3	wgs	PATRIC	1849104 tax ID	*

[Ref.: #25044]

GC-content

65 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 GenomeNet Sporulation v. 1 based on: Mesorhizobium sediminum strain KCTC 42205 PATRIC: 1849104.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Mesorhizobium sediminum strain KCTC 42205 PATRIC: 1849104.3
[Ref.: #69480]	motile	yes	86.138	no
[Ref.: #69480]	gram-positive	no	98.135	yes
[Ref.: #69480]	anaerobic	no	97.514	no
[Ref.: #69480]	aerobic	yes	94.686	yes
[Ref.: #69480]	halophile	no	83.452	no
[Ref.: #69480]	spore-forming	no	96.717	yes
[Ref.: #69480]	glucose-util	yes	91.614	no
[Ref.: #69480]	flagellated	no	72.835	no
[Ref.: #69480]	thermophile	no	98.826	yes
[Ref.: #69480]	glucose-ferment	no	92.754	yes

Availability in culture collections External links

[Ref.: #25044]

Culture collection no.

YIM M12096, CCTCC AB 2014219, KCTC 42205, JCM 30310

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Mesorhizobium microcysteis sp. nov., isolated from a culture of Microcystis aeruginosa.	Jung J, Seo YL, Kim KR, Park HY, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.004847	2021	*
Phylogeny	Mesorhizobium sediminum sp. nov., isolated from deep-sea sediment.	Yuan CG, Jiang Z, Xiao M, Zhou EM, Kim CJ, Hozzein WN, Park DJ, Zhi XY, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001432	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 )

#25044

C. G. J. Yuan, Z.,Xiao, M.,Zhou, E. M.,Kim, C. J.,Hozzein, W. N.,Park, D. J.,Zhi, X. Y.,Li, W. J.: Mesorhizobium sediminum sp. nov., isolated from deep-sea sediment. IJSEM 66: 4797 - 4802 2016 ( DOI 10.1099/ijsem.0.001432 , PubMed 27535803 )

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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Mesorhizobium sediminum strain KCTC 42205

Mesorhizobium sediminum strain KCTC 42205

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