Archive BacDiveID:10.13145/bacdive13671.20230509.8.1

Strain identifier

BacDive ID: 13671

Type strain:

Species: Sedimentitalea nanhaiensis

Strain Designation: NH52F

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)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 17585

BacDive-ID: 13671

DSM-Number: 24252

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

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

NCBI tax id

NCBI tax id	Matching level
999627	species
571166	strain

strain history

@ref: 17585
history: <- LMG <- B. Wang, Third Inst. Oceanography, China; NH52F <- Sun, Liu and Du, Third Inst. Oceanography, China

doi: 10.13145/bacdive13671.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Rhodobacterales
family: Roseobacteraceae
genus: Sedimentitalea
species: Sedimentitalea nanhaiensis
full scientific name: Sedimentitalea nanhaiensis (Sun et al. 2010) Breider et al. 2014
synonyms
- @ref: 20215
- synonym: Leisingera nanhaiensis

@ref: 17585

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Sedimentitalea

species: Sedimentitalea nanhaiensis

full scientific name: Sedimentitalea nanhaiensis (Sun et al. 2010) Breider et al. 2014

strain designation: NH52F

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
29295	negative	2.28 µm	0.71 µm	rod-shaped	yes
69480	negative					99.999

colony morphology

@ref: 17585
incubation period: 1-2 days

pigmentation

@ref: 29295
production: yes

multimedia

@ref: 66793
multimedia content: EM_DSM_24252_1.jpg
caption: electron microscopic image
intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 17585
name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
growth: yes
link: https://mediadive.dsmz.de/medium/514
composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
17585	positive	growth	28	mesophilic
29295	positive	growth	04-37
29295	positive	optimum	25	mesophilic

culture pH

@ref	ability	type	pH	PH range
29295	positive	growth	6-9.3	alkaliphile
29295	positive	optimum	7.75

Physiology and metabolism

oxygen tolerance

@ref: 29295
oxygen tolerance: aerobe

spore formation

@ref	spore formation	confidence
69481	no	99
69480	no	99.999

halophily

@ref	salt	growth	tested relation	concentration
29295	NaCl	positive	growth	0.6-6 %
29295	NaCl	positive	optimum	2.5 %

enzymes

@ref	value	activity	ec
29295	acid phosphatase	+	3.1.3.2
29295	alkaline phosphatase	+	3.1.3.1
29295	catalase	+	1.11.1.6
29295	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

isolation

@ref: 17585
sample type: sediment
geographic location: South China Sea
country: China
origin.country: CHN
continent: Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Sediment

taxonmaps

@ref: 69479
File name: preview.99_3412.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_97;97_2136;98_2617;99_3412&stattab=map
Last taxonomy: Sedimentitalea nanhaiensis subclade
16S sequence: FJ232451
Sequence Identity:
Total samples: 1562
soil counts: 75
aquatic counts: 1427
animal counts: 54
plant counts: 6

Safety information

risk assessment

@ref: 17585
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 17585
description: Leisingera nanhaiensis DSM 24252 strain NH52F 16S ribosomal RNA gene, partial sequence
accession: FJ232451
length: 1429
database: ena
NCBI tax ID: 571166

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Sedimentitalea nanhaiensis DSM 24252	GCA_000473225	scaffold	ncbi	571166
66792	Leisingera nanhaiensis DSM 24252	571166.3	wgs	patric	571166
66792	Sedimentitalea nanhaiensis DSM 24252	2521172577	draft	img	571166

GC content

@ref: 29295
GC-content: 60.5

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	99	no
motile	no	52.747	yes
flagellated	no	90.54	no
gram-positive	no	97.825	no
anaerobic	no	98.467	yes
aerobic	yes	92.082	yes
halophile	yes	75.74	no
spore-forming	no	96.7	no
thermophile	no	98.098	no
glucose-util	yes	57.905	no
glucose-ferment	no	90.953	no

External links

@ref: 17585

culture collection no.: DSM 24252, CCTCC AB 208316, LMG 24841, MCCC 1A04178

straininfo link

@ref: 82854
straininfo: 360391

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19651744	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	Base Composition, Base Sequence, China, DNA, Bacterial/chemistry, Geologic Sediments/microbiology, Molecular Sequence Data, Oceans and Seas, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/physiology, Seawater/microbiology, Water Microbiology	Genetics
Genetics	25197454	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	27226032	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	Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Decapodiformes/microbiology, Fatty Acids/chemistry, Intestines/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, Republic of Korea, Rhodobacteraceae/classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistry	Transcriptome
Phylogeny	31913437	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	Base Composition, China, Chromosomes, Bacterial, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Phospholipids/analysis, Phylogeny, Plasmids/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/isolation & purification/physiology, Seawater/microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
17585	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24252)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-24252
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29295	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	25711	28776041
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life		28604660	35: 676-683 2017
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates		33211880	Nucleic Acids Res. 49: D498-D508 2020
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
82854	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID360391.1	StrainInfo: A central database for resolving microbial strain identifiers

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

colony morphology

pigmentation

multimedia

Culture and growth conditions

culture medium

culture temp

culture pH

Physiology and metabolism

oxygen tolerance

spore formation

halophily

enzymes

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference