Halomonas zincidurans (CGMCC 1.12450, JCM 18472, B6)

Name: Halomonas zincidurans (CGMCC 1.12450, JCM 18472, B6)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134028

Type strain

Strain Designation B6

Culture col. no. CGMCC 1.12450 JCM 18472 B6

NCBI tax ID(s) 1178777

Special Collections JCM Literature strains

Links

Halomonas zincidurans B6 is an aerobe, Gram-negative, motile prokaryote that was isolated from marine sediment.

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

Name and taxonomic classification

SI-ID 27844

JCM 18472

@ref 20215

Last LPSN update 2025-12-16 10:01:57

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Halomonadaceae

Genus Halomonas

Species Halomonas zincidurans

Full scientific name Halomonas zincidurans Xu et al. 2013

Synonyms (1)

Modicisalibacter zincidurans

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31086	negative	1.05 µm	0.4 µm	rod-shaped
125438	negative				99.969
125439	negative				98.8

Pigmentation

31086

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
31086	positive	growth	04-37
31086	positive	optimum	35	mesophilic
67770	positive	growth	35	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31086	positive	optimum	7
31086	positive	growth	5.0-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31086	aerobe
125439	aerobe	94.8

Spore formation

@ref	Spore formation	Confidence
125438		92.017
125439		99.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31086	NaCl	positive	growth	0.5-15 %
31086	NaCl	positive	optimum	5 %

Observation

@ref	Observation
31086	aggregates in clumps
67770	quinones: Q-9

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31086	30089 ChEBI	acetate	+	carbon source
31086	16449 ChEBI	alanine	+	carbon source
31086	22599 ChEBI	arabinose	+	carbon source
31086	29016 ChEBI	arginine	+	carbon source
31086	17057 ChEBI	cellobiose	+	carbon source
31086	16947 ChEBI	citrate	+	carbon source
31086	16236 ChEBI	ethanol	+	carbon source
31086	28757 ChEBI	fructose	+	carbon source
31086	24265 ChEBI	gluconate	+	carbon source
31086	17234 ChEBI	glucose	+	carbon source
31086	29987 ChEBI	glutamate	+	carbon source
31086	17754 ChEBI	glycerol	+	carbon source
31086	15428 ChEBI	glycine	+	carbon source
31086	17306 ChEBI	maltose	+	carbon source
31086	29864 ChEBI	mannitol	+	carbon source
31086	37684 ChEBI	mannose	+	carbon source
31086	17632 ChEBI	nitrate	+	reduction
31086	18257 ChEBI	ornithine	+	carbon source
31086	17272 ChEBI	propionate	+	carbon source
31086	15361 ChEBI	pyruvate	+	carbon source
31086	15963 ChEBI	ribitol	+	carbon source
31086	33942 ChEBI	ribose	+	carbon source
31086	17814 ChEBI	salicin	+	carbon source
31086	17822 ChEBI	serine	+	carbon source
31086	30911 ChEBI	sorbitol	+	carbon source
31086	30031 ChEBI	succinate	+	carbon source
31086	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31086	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
31086	acid phosphatase	+	3.1.3.2
31086	alkaline phosphatase	+	3.1.3.1
31086	catalase	+	1.11.1.6
31086	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type
31086	marine sediment
67770	Deep sea sediment from the South Atlantic Ocean

Taxonmaps

69479

Global distribution of 16S sequence JQ781698 (>99% sequence identity) for Halomonas zincidurans from Microbeatlas

Aquatic Samples	350
Soil Samples	23
Animal Samples	19
Plant Samples	13
Total Samples	405

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	B6 assembly for Halomonas zincidurans B6	contig	GCA_000731955	1446475.3	2585427838	1446475	77.98
124043	ASM3954374v1 assembly for Modicisalibacter zincidurans JCM 18472	contig	GCA_039543745			1178777	67.89

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31086	Halomonas zincidurans strain B6 16S ribosomal RNA gene, partial sequence	JQ781698	1477		1446475

GC content

@ref	GC-content (mol%)	Method
31086	61.1
67770	61.1	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: Halomonas zincidurans B6
NCBI: GCA_000731955

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.30	no
125439	motility	BacteriaNetⓘ	yes	82.70	no
125439	gram_stain	BacteriaNetⓘ	negative	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	94.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Halomonas zincidurans B6
PATRIC: 1446475.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.97	no
125438	anaerobic	anaerobicⓘ	no	97.18	yes
125438	spore-forming	spore-formingⓘ	no	92.02	no
125438	aerobic	aerobicⓘ	yes	80.96	no
125438	thermophilic	thermophileⓘ	no	95.46	yes
125438	flagellated	motile2+ⓘ	yes	81.80	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	High quality draft genome sequence of the heavy metal resistant bacterium Halomonas zincidurans type strain B6(T).	Huo YY, Li ZY, Cheng H, Wang CS, Xu XW.	Stand Genomic Sci	10.1186/1944-3277-9-30	2014
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	Isolation and Identification of Mercury-Tolerant Bacteria LBA119 from Molybdenum-Lead Mining Soils and Their Removal of Hg².	Yao H, Wang H, Ji J, Tan A, Song Y, Chen Z.	Toxics	10.3390/toxics11030261	2023
Phylogeny	A halophilic bacterium inhabiting the warm, CaCl2-rich brine of the perennially ice-covered Lake Vanda, McMurdo Dry Valleys, Antarctica.	Tregoning GS, Kempher ML, Jung DO, Samarkin VA, Joye SB, Madigan MT.	Appl Environ Microbiol	10.1128/aem.03968-14	2015
Phylogeny	Halomonas radicis sp. nov., isolated from Arthrocnemum macrostachyum growing in the Odiel marshes(Spain) and emended descriptions of Halomonas xinjiangensis and Halomonas zincidurans.	Navarro-Torre S, Carro L, Rodriguez-Llorente ID, Pajuelo E, Caviedes MA, Igual JM, Klenk HP, Montero-Calasanz MDC.	Int J Syst Evol Microbiol	10.1099/ijsem.0.003742	2020
Phylogeny	Halomonas zincidurans sp. nov., a heavy-metal-tolerant bacterium isolated from the deep-sea environment.	Xu L, Xu XW, Meng FX, Huo YY, Oren A, Yang JY, Wang CS	Int J Syst Evol Microbiol	10.1099/ijs.0.051656-0	2013

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 )
#31086	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 #27415 (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) .
#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 .
#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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Halomonas zincidurans (CGMCC 1.12450, JCM 18472, B6)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_000731955

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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