Name: Sedimentitalea nanhaiensis NH52F
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13671

Type strain:

Species: Sedimentitalea nanhaiensis

Strain Designation: NH52F

Culture col. no.: DSM 24252, CCTCC AB 208316, LMG 24841, MCCC 1A04178

Strain history: <- LMG <- B. Wang, Third Inst. Oceanography, China; NH52F <- Sun, Liu and Du, Third Inst. Oceanography, China

NCBI tax ID(s): 571166 (strain), 999627 (species)

SI-ID 360391

LMG 24841, DSM 24252

Section

Sedimentitalea nanhaiensis NH52F is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment.

Gram-negative
motile
rod-shaped
aerobe
mesophilic
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	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Sedimentitalea*
	Species	**Sedimentitalea nanhaiensis**
	Full Scientific Name (LPSN)	Sedimentitalea nanhaiensis (Sun et al. 2010) Breider et al. 2014

Synonym

Leisingera nanhaiensis

Information on morphological and physiological properties Morphology

[Ref.: #29295]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #29295]	Cell length	2.28 µm

[Ref.: #29295]	Cell width	0.71 µm

[Ref.: #29295]	Cell shape	rod-shaped

[Ref.: #29295]	Motility	yes

[Ref.: #17585]

Incubation period

1-2 days

[Ref.: #29295]

Pigment production

yes

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17585]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #17585]

Culture medium growth

[Ref.: #17585]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17585]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17585]	growth	28 °C
[Ref.: #29295]	growth	04-37 °C
[Ref.: #29295]	optimum	25 °C

[Ref.: #17585]	Temperature range	mesophilic
[Ref.: #29295]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29295]			optimum	7.75
[Ref.: #29295]			growth	6-9.3

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29295]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29295]		NaCl		growth	0.6-6	%
[Ref.: #29295]		NaCl		optimum	2.5	%

	Enzyme	Enzyme activity	EC number
[Ref.: #29295]	acid phosphatase	+	3.1.3.2
[Ref.: #29295]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29295]	catalase	+	1.11.1.6
[Ref.: #29295]	cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	100	9 of 9
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	methionine metabolism	88.46	23 of 26
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	purine metabolism	79.79	75 of 94
[Ref.: #66794]	histidine metabolism	79.31	23 of 29
[Ref.: #66794]	arginine metabolism	79.17	19 of 24
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	carnitine metabolism	75	6 of 8
[Ref.: #66794]	toluene degradation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	lysine metabolism	73.81	31 of 42
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	69.23	9 of 13
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	oxidative phosphorylation	67.03	61 of 91
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	phenol degradation	65	13 of 20
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	3-chlorocatechol degradation	60	3 of 5
[Ref.: #66794]	3-phenylpropionate degradation	60	9 of 15
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	degradation of sugar acids	52	13 of 25
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	androgen and estrogen metabolism	50	8 of 16
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	ginsenoside metabolism	25	4 of 16
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
		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.: #17585]	Sample type/isolated from	sediment
[Ref.: #17585]	Geographic location (country and/or sea, region)	South China Sea
[Ref.: #17585]	Country	China
[Ref.: #17585]	Country ISO 3 Code	CHN
[Ref.: #17585]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ232451 (>99% sequence identity) for Sedimentitalea nanhaiensis subclade from Microbeatlas

Aquatic Samples	1427
Soil Samples	75
Animal Samples	54
Plant Samples	6
Total Samples	1562

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #17585]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #17585]	Leisingera nanhaiensis DSM 24252 strain NH52F 16S ribosomal RNA gene, partial sequence	FJ232451	1429	ENA	571166 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sedimentitalea nanhaiensis DSM 24252	GCA_000473225	scaffold	GenBank	571166 tax ID	*
[Ref.: #66792]	Leisingera nanhaiensis DSM 24252	571166.3	wgs	PATRIC	571166 tax ID	*
[Ref.: #66792]	Sedimentitalea nanhaiensis DSM 24252	2521172577	draft	JGI IMG/M	571166 tax ID	*

[Ref.: #29295]

GC-content

60.5 mol%

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: Sedimentitalea nanhaiensis DSM 24252 DSM 24252 NCBI: GCA_000473225.1
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sedimentitalea nanhaiensis DSM 24252 DSM 24252 NCBI: GCA_000473225.1
[Ref.: #69480]	motile	no	52.747	yes
[Ref.: #69480]	flagellated	no	90.54	no
[Ref.: #69480]	gram-positive	no	97.825	no
[Ref.: #69480]	anaerobic	no	98.467	yes
[Ref.: #69480]	aerobic	yes	92.082	yes
[Ref.: #69480]	halophile	yes	75.74	no
[Ref.: #69480]	spore-forming	no	96.7	no
[Ref.: #69480]	thermophile	no	98.098	no
[Ref.: #69480]	glucose-util	yes	57.905	no
[Ref.: #69480]	glucose-ferment	no	90.953	no

Availability in culture collections External links

[Ref.: #17585]

Culture collection no.

DSM 24252, CCTCC AB 208316, LMG 24841, MCCC 1A04178

[Ref.: #82854]

SI-ID 360391

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Polyphasic taxonomic analysis of Parasedimentitalea marina gen. nov., sp. nov., a psychrotolerant bacterium isolated from deep sea water of the New Britain Trench.	Ding W, Liu P, Xu Y, Fang J, Cao J	FEMS Microbiol Lett	10.1093/femsle/fnaa004	2019	*
Phylogeny	Sedimentitalea todarodis sp. nov., isolated from the intestinal tract of a Japanese flying squid.	Kim HS, Hyun DW, Lee JY, Kim PS, Whon TW, Kang W, Bae JW	Int J Syst Evol Microbiol	10.1099/ijsem.0.001188	2016	*
Genetics	Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment.	Breider S, Teshima H, Petersen J, Chertkov O, Dalingault H, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Tindall BJ, Kyrpides NC, Woyke T, Simon M, Goker M, Klenk HP, Brinkhoff T	Stand Genomic Sci	10.4056/sigs.3828824	2014	*
Phylogeny	Leisingera nanhaiensis sp. nov., isolated from marine sediment.	Sun F, Wang B, Liu X, Lai Q, Du Y, Li G, Luo J, Shao Z	Int J Syst Evol Microbiol	10.1099/ijs.0.010439-0	2009	*

References

#17585

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24252

#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 )

#29295

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25711 (see below)

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 )

#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 )

#82854

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID360391.1 )

#25711

IJSEM 275 2010 ( DOI 10.1099/ijs.0.010439-0 , PubMed 19651744 )

* These data were automatically processed and therefore are not curated

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Sedimentitalea nanhaiensis DSM 24252 DSM 24252

Sedimentitalea nanhaiensis DSM 24252 DSM 24252

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