Halomonas nanhaiensis (DSM 25561, CCTCC AB 2012911, JCM 18142)

Name: Halomonas nanhaiensis (DSM 25561, CCTCC AB 2012911, JCM 18142)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24094

Type strain

Culture col. no. DSM 25561 CCTCC AB 2012911 JCM 18142 YIM 13059 YIM M 13059

NCBI tax ID(s) 1258546

Special Collections DSMZ JCM

History DSMZ <- S.-K. Tang, YIM; YIM M13059 <- D.-F. Zhang JCM <-- S.-K. Tang YIM M13059.

Links

Halomonas nanhaiensis DSM 25561 is a bacterium that was isolated from marine sediment.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402803

JCM 18142,DSM 25561

@ref 20215

Last LPSN update 2026-05-29 08:30:33

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Halomonadaceae

Genus Halomonas

Species Halomonas nanhaiensis

Full scientific name Halomonas nanhaiensis Long et al. 2013

Synonyms (1)

Vreelandella nanhaiensis

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	93.982
125438	negative	99.969

Colony morphology

20974

Incubation period3-7 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
20974	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65; with strain-specific modifications) Composition: Sea Salt 25.0 g/l Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
20974	MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)	Medium recipe at MediaDive	Name: MEDIUM 514 plus additional salt (DSMZ Medium 514b) Composition: NaCl 19.45 g/l Agar 17.5 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
20974	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	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 (°C)
20974	positive	growth	28
20974	positive	growth	5-28
67770	positive	growth	30

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		98.944

Observation

67770

Observationquinones: Q-9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
20974	marine sediment	South China Sea (116° 8.923' E 21° 5.905' N) at a depth of 310 m	China	CHN	Asia	21.0984	116.149 21.0984/116.149
67770	Sediment sample collected from the South China Sea (21° 5.905' N 116° 8.923' E)					21.0984	116.149 21.0984/116.149

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20974	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM399018v1 assembly for Vreelandella nanhaiensis JCM 18142	scaffold	GCA_003990185	2498860.3	2885257956	1258546	70.19

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20974	Halomonas nanhaiensis strain YIM M 13059 16S ribosomal RNA gene, partial sequence	JX870002	1537		1258546

GC content

@ref	GC-content (mol%)	Method
20974	54.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM399018v1 assembly for Vreelandella nanhaiensis JCM 18142
NCBI: GCA_003990185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	93.98	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	88.03	no
125439	motility	BacteriaNetⓘ	yes	63.39	no
125439	spore_formation	BacteriaNetⓘ	no	98.94	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halomonas nanhaiensis JCM 18142
NCBI: GCA_003990185.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.97	no
125438	anaerobic	anaerobicⓘ	no	96.58	no
125438	aerobic	aerobicⓘ	yes	83.49	no
125438	spore-forming	spore-formingⓘ	no	86.49	no
125438	thermophilic	thermophileⓘ	no	98.61	no
125438	flagellated	motile2+ⓘ	yes	81.25	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Validation List no. 216. Valid publication of new names and new combinations effectively published outside the IJSEM.	Oren A, Goker M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006229	2024
Genetics	A long-awaited taxogenomic investigation of the family Halomonadaceae.	de la Haba RR, Arahal DR, Sanchez-Porro C, Chuvochina M, Wittouck S, Hugenholtz P, Ventosa A.	Front Microbiol	10.3389/fmicb.2023.1293707	2023
Phylogeny	Halomonas songnenensis sp. nov., a moderately halophilic bacterium isolated from saline and alkaline soils.	Jiang J, Pan Y, Hu S, Zhang X, Hu B, Huang H, Hong S, Meng J, Li C, Wang K	Int J Syst Evol Microbiol	10.1099/ijs.0.056499-0	2014
Phylogeny	Halomonas nanhaiensis sp. nov., a halophilic bacterium isolated from a sediment sample from the South China Sea.	Long MR, Zhang DF, Yang XY, Zhang XM, Zhang YG, Zhang YM, Zhu H, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-013-9879-3	2013
Phylogeny	Halomonas populi sp. nov. isolated from Populus euphratica.	Xu L, Ying JJ, Fang YC, Zhang R, Hua J, Wu M, Han BN, Sun C	Arch Microbiol	10.1007/s00203-021-02704-w	2021

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 )
#20974	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25561
#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;
#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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Halomonas nanhaiensis (DSM 25561, CCTCC AB 2012911, JCM 18142)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003990185

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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