Limimaricola hongkongensis (DSM 17492, JCM 12479, NRRL B-41039)

Name: Limimaricola hongkongensis (DSM 17492, JCM 12479, NRRL B-41039)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13675

Type strain

Strain Designation UST950701-009P

Culture col. no. DSM 17492 JCM 12479 NRRL B-41039 UST950701-009P CIP 108639

NCBI tax ID(s) 1122180 278132

Special Collections DSMZ JCM CIP Literature strains

History <- M. M. Y. Tsoi, Dept. Biol., UST Hong Kong; UST950701-009P <- S. C. K. Lau S. Lau UST950701-009P. CIP <- 2005, JCM <- S. Lau: strain UST950701-009P

Links

Limimaricola hongkongensis UST950701-009P is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from 7-day-old marine biofilm in Hong Kong waters.

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

Name and taxonomic classification

SI-ID 134437

JCM 12479,NRRL B-41039,CIP 108639,DSM 17492

@ref 20215

Last LPSN update 2026-02-09 11:21:12

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Roseobacteraceae

Genus Limimaricola

Species Limimaricola hongkongensis

Full scientific name Limimaricola hongkongensis (Lau et al. 2004) Wirth and Whitman 2018

Synonyms (1)

Loktanella hongkongensis

BacDive ID	Other strains from **Limimaricola hongkongensis** (1)	Type strain
13676	L. hongkongensis UST950701-009W, DSM 17493, JCM 12480, NRRL ...

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31318	negative	rod-shaped
119962	negative	rod-shaped
125438	negative		97.733
125439	negative		98.6

Pigmentation

31318

Productionyes

Multimedia

@ref:	66793
multimedia content:	EM_DSM_17492_1.jpg
multimedia.multimedia content:	EM_DSM_17492_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_17492_2.jpg
multimedia.multimedia content:	EM_DSM_17492_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_17492_3.jpg
multimedia.multimedia content:	EM_DSM_17492_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_17492_4.jpg
multimedia.multimedia content:	EM_DSM_17492_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_17492_5.jpg
multimedia.multimedia content:	EM_DSM_17492_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7019	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
36757	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
119962	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
7019	positive	growth	30
31318	positive	growth	08-44
31318	positive	optimum	26
36757	positive	growth	30
67770	positive	growth	30
119962	positive	growth	15-37
119962	negative	growth	5
119962	negative	growth	41

Culture pH

@ref	Ability	Type	PH	PH range
31318	positive	optimum	7.5
31318	positive	growth	05-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
31318	aerobe
119962	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
31318
125439		96.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31318	NaCl	positive	growth	02-14 %
31318	NaCl	positive	optimum	8 %
119962	NaCl	positive	growth	0-10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
31318	22599 ChEBI	arabinose	+	carbon source
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
119962	16947 ChEBI	citrate	-	carbon source
68371	17108 ChEBI	D-arabinose	+	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	+	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68371	62318 ChEBI	D-lyxose	+	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68369	16899 ChEBI	D-mannitol	+	assimilation	from API 20NE
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68369	16024 ChEBI	D-mannose	+	assimilation	from API 20NE
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
119962	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
31318	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	+	builds acid from	from API 50CH acid
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
31318	17234 ChEBI	glucose	+	carbon source
119962	17234 ChEBI	glucose	-	degradation
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	+	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
31318	29864 ChEBI	mannitol	+	carbon source
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
119962	17632 ChEBI	nitrate	+	reduction
119962	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
119962	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	+	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
119962	132112 ChEBI	sodium thiosulfate	-	builds gas from
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
31318	17992 ChEBI	sucrose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
31318	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
119962	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test	Voges-proskauer-test	Methylred-test
119962	15688 ChEBI	acetoin		-
119962	17234 ChEBI	glucose			-
68369	35581 ChEBI	indole	-			from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
119962	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
119962	amylase	-
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
119962	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119962	caseinase	-	3.4.21.50
31318	catalase	+	1.11.1.6
119962	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31318	cytochrome oxidase	+	1.9.3.1
119962	gamma-glutamyltransferase	+	2.3.2.2
119962	gelatinase	-
68369	gelatinase	-		from API 20NE
119962	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119962	lipase	-
68382	lipase (C 14)	-		from API zym
119962	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
119962	ornithine decarboxylase	-	4.1.1.17
119962	oxidase	+
119962	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
119962	tryptophan deaminase	-
119962	tween esterase	-
119962	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
7019	-	+	-	+/-	-	+	-	-	-	-	-	-	+	-	-	+	-	-	-	-
119962	-	+	+	+	-	+	+	-	-	-	-	-	+	-	-	+	-	-	+	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
7019	-	-	-	-	-	+	-	+	+	-	+	+	-	+	+	-	+/-	+	+/-	-	not determinedn.d.

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
119962	not determinedn.d.	+/-	-	+	+	+	+/-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+/-	+/-	-	-	+/-	-	-	-	-	-	+	+/-	+	-	-	-	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Biofilm	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7019	7-day-old marine biofilm in Hong Kong waters		China	CHN	Asia
67770	Marine biofilm in Hong Kong waters
119962	Marine biofilms	Hong Kong	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AY600300 (>99% sequence identity) for Limimaricola from Microbeatlas

Aquatic Samples	3059
Soil Samples	214
Animal Samples	378
Plant Samples	76
Total Samples	3727

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7019	1	Risk group (German classification) According to TRBA 466
119962	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM36500v1 assembly for Limimaricola hongkongensis DSM 17492 UST950701-009P	scaffold	GCA_000365005	1122180.3	2517434011	1122180	76.11
66792	Lokhon assembly for Limimaricola hongkongensis DSM 17492	scaffold	GCA_000600975	1122180.6	2982337018	1122180	75.88

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Loktanella hongkongensis strain NRRL B-41039 16S ribosomal RNA gene, partial sequence	DQ915609	1306		278132
7019	Loktanella hongkongensis strain UST950701-009P 16S ribosomal RNA gene, partial sequence	AY600300	1407		278132

GC content

@ref	GC-content (mol%)	Method
7019	65.9
67770	65.5-66.3	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: Limimaricola hongkongensis DSM 17492
NCBI: GCA_000600975

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	84.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.60	no
125439	motility	BacteriaNetⓘ	yes	73.60	no
125439	spore_formation	BacteriaNetⓘ	no	96.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Limimaricola hongkongensis DSM 17492 DSM 17492
NCBI: GCA_000600975.2

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.73	yes
125438	anaerobic	anaerobicⓘ	no	93.27	yes
125438	aerobic	aerobicⓘ	yes	82.95	no
125438	spore-forming	spore-formingⓘ	no	88.94	yes
125438	thermophilic	thermophileⓘ	no	92.61	no
125438	flagellated	motile2+ⓘ	no	56.87	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome sequence of the pink-pigmented marine bacterium Loktanella hongkongensis type strain (UST950701-009P(T)), a representative of the Roseobacter group.	Lau SC, Riedel T, Fiebig A, Han J, Huntemann M, Petersen J, Ivanova NN, Markowitz V, Woyke T, Goker M, Kyrpides NC, Klenk HP, Qian PY	Stand Genomic Sci	10.1186/s40793-015-0050-9	2015
Phylogeny	Limimaricola litoreus sp. nov., isolated from intertidal sand of the Yellow Sea.	Shao X, Meng D, Lei JX, Ding YY, Su JY, Wang YN, Li Y.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005772	2023
Phylogeny	Marivivens aquimaris sp. nov., isolated from seawater.	Kim JA, Lee B, Kang JY, Song JJ, Choi JH	Arch Microbiol	10.1007/s00203-021-02305-7	2021
Phylogeny	Loktanella soesokkakensis sp. nov., isolated from the junction between the North Pacific Ocean and a freshwater spring.	Park S, Lee JS, Lee KC, Yoon JH	Antonie Van Leeuwenhoek	10.1007/s10482-013-9962-9	2013
Phylogeny	Loktanella cinnabarina sp. nov., isolated from a deep subseafloor sediment, and emended description of the genus Loktanella.	Tsubouchi T, Shimane Y, Mori K, Miyazaki M, Tame A, Uematsu K, Maruyama T, Hatada Y	Int J Syst Evol Microbiol	10.1099/ijs.0.043174-0	2012
Phylogeny	Loktanella hongkongensis sp. nov., a novel member of the alpha-Proteobacteria originating from marine biofilms in Hong Kong waters.	Lau SCK, Tsoi MMY, Li X, Plakhotnikova I, Wu M, Wong PK, Qian PY	Int J Syst Evol Microbiol	10.1099/ijs.0.63294-0	2004

References

#7019	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17492
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#27633	IJSEM 2281 2004 ( DOI 10.1099/ijs.0.63294-0 , PubMed 15545471 )
#31318	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 #27633
#36757	; Curators of the CIP;
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68369	Automatically annotated from API 20NE .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#119962	Collection of Institut Pasteur ; Curators of the CIP; CIP 108639
#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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Limimaricola hongkongensis (DSM 17492, JCM 12479, NRRL B-41039)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000365005

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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