Pelagibacterium halotolerans (DSM 22347, CGMCC 1.7692, JCM 15775)

Name: Pelagibacterium halotolerans (DSM 22347, CGMCC 1.7692, JCM 15775)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6198

Type strain

Strain Designation B2

Culture col. no. DSM 22347 CGMCC 1.7692 JCM 15775 B2

NCBI tax ID(s) 1082931 531813

Special Collections DSMZ JCM

History <- X.-W. Xu, Zhejiang Univ., Zijingang Campus, P.R. China; B2 X.-W. Xu B2.

Links

Pelagibacterium halotolerans B2 is a mesophilic prokaryote that was isolated from Sea water.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 400210

JCM 15775,DSM 22347

@ref 20215

Last LPSN update 2026-02-09 11:19:09

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Devosiaceae

Genus Pelagibacterium

Species Pelagibacterium halotolerans

Full scientific name Pelagibacterium halotolerans Xu et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	96.6
125439	negative	97.1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16304	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)	Range
16304	positive	growth	28	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	90.6

Spore formation

@ref	Spore formation	Confidence
125438		94.369
125439		92.4

Observation

67770

Observationquinones: Q-10, Q-9

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cardiolipin biosynthesis	100	7 of 7
66794	formaldehyde oxidation	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	quinate degradation	100	2 of 2
66794	4-hydroxymandelate degradation	100	9 of 9
66794	ethanol fermentation	100	2 of 2
66794	allantoin degradation	100	9 of 9
66794	cyanate degradation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	gallate degradation	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	ppGpp biosynthesis	100	4 of 4
66794	resorcinol degradation	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	creatinine degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	lactate fermentation	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	palmitate biosynthesis	95.45	21 of 22
66794	leucine metabolism	92.31	12 of 13
66794	vitamin B12 metabolism	91.18	31 of 34
66794	proline metabolism	90.91	10 of 11
66794	pentose phosphate pathway	90.91	10 of 11
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	cellulose degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	degradation of sugar acids	80	20 of 25
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	purine metabolism	79.79	75 of 94
66794	alanine metabolism	79.31	23 of 29
66794	photosynthesis	78.57	11 of 14
66794	glutathione metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	pyrimidine metabolism	75.56	34 of 45
66794	ketogluconate metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	biotin biosynthesis	75	3 of 4
66794	vitamin B6 metabolism	72.73	8 of 11
66794	tyrosine metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	degradation of pentoses	71.43	20 of 28
66794	urea cycle	69.23	9 of 13
66794	oxidative phosphorylation	69.23	63 of 91
66794	octane oxidation	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	IAA biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	lysine metabolism	66.67	28 of 42
66794	UDP-GlcNAc biosynthesis	66.67	2 of 3
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	methionine metabolism	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	gluconeogenesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	vitamin B1 metabolism	61.54	8 of 13
66794	sulfate reduction	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	flavin biosynthesis	60	9 of 15
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	lipid metabolism	58.06	18 of 31
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	d-mannose degradation	55.56	5 of 9
66794	nitrate assimilation	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	phenol degradation	55	11 of 20
66794	metabolism of disaccharids	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of sugar alcohols	43.75	7 of 16
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	ascorbate metabolism	40.91	9 of 22
66794	3-chlorocatechol degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	bile acid biosynthesis, neutral pathway	35.29	6 of 17
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	polyamine pathway	30.43	7 of 23
66794	starch degradation	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	toluene degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
16304	Sea water	East China Sea (30° 58' 16'' N 125° 59' 24'' E)	China	CHN	Asia	30.9711	125.99 30.9711/125.99
67770	Seawater sample collected from the East China Sea

Taxonmaps

69479

Global distribution of 16S sequence EU709017 (>99% sequence identity) for Pelagibacterium halotolerans from Microbeatlas

Aquatic Samples	38
Soil Samples	17
Animal Samples	19
Plant Samples	3
Total Samples	77

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16304	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM23055v1 assembly for Pelagibacterium halotolerans B2	complete	GCA_000230555	1082931.4	2511231054	1082931	97.94

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16304	Pelagibacterium halotolerans B2 16S ribosomal RNA gene, partial sequence	EU709017	1408		1082931

GC content

@ref	GC-content (mol%)	Method
16304	59.3	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: Pelagibacterium halotolerans B2
PATRIC: 1082931.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.60	no
125439	gram_stain	BacteriaNetⓘ	negative	97.10	no
125439	motility	BacteriaNetⓘ	yes	69.40	no
125439	spore_formation	BacteriaNetⓘ	no	92.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pelagibacterium halotolerans B2 B2
NCBI: GCA_000230555.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.60	no
125438	anaerobic	anaerobicⓘ	no	94.47	no
125438	aerobic	aerobicⓘ	yes	84.76	no
125438	spore-forming	spore-formingⓘ	no	94.37	no
125438	thermophilic	thermophileⓘ	no	95.96	yes
125438	flagellated	motile2+ⓘ	yes	66.59	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium deserti sp. Nov Isolated from Biological Soil Crusts Collected at Mu Us Sandy Land, China.	Liu L, Liang L, Xu L, Chi M, Zhang X, Li L.	Curr Microbiol	10.1007/s00284-019-01831-4	2020
	Bioremediation of acetamiprid and sulfoxaflor co-contamination by Ensifer sp. DA6 and characterization of a novel nitrile hydratase involved.	Yang W, Kang J, Shao Y, Geng Y, Zhang Y, Liu R, Chen G.	Front Microbiol	10.3389/fmicb.2025.1705774	2025
Enzymology	Characterization of a novel metallo-beta-lactamases fold hydrolase from Pelagibacterium halotolerans, a marine halotolerant bacterium isolated from East China Sea.	Zheng B, Jiang X, Xu Z, Fang Y, Li L.	Extremophiles	10.1007/s00792-015-0795-5	2016
Metabolism	Functional Role of Bacteria from Invasive Phragmites australis in Promotion of Host Growth.	Soares MA, Li HY, Kowalski KP, Bergen M, Torres MS, White JF.	Microb Ecol	10.1007/s00248-016-0793-x	2016
Enzymology	Bacterial diversity and biopotentials of Hamtah glacier cryoconites, Himalaya.	Singh P, Singh SM, Segawa T, Singh PK.	Front Microbiol	10.3389/fmicb.2024.1362678	2024
Metabolism	Enhanced xylitol production: Expression of xylitol dehydrogenase from Gluconobacter oxydans and mixed culture of resting cell.	Qi XH, Zhu JF, Yun JH, Lin J, Qi YL, Guo Q, Xu H.	J Biosci Bioeng	10.1016/j.jbiosc.2016.02.009	2016
Enzymology	Cloning, expression and characterization of a halotolerant esterase from a marine bacterium Pelagibacterium halotolerans B2T.	Jiang X, Huo Y, Cheng H, Zhang X, Zhu X, Wu M.	Extremophiles	10.1007/s00792-012-0442-3	2012
Enzymology	Pelagibacterium nitratireducens sp.nov., a marine Alphaproteobacterium isolated from the East China Sea.	Li Q, Xu Y, Liu K, Cai L, Fu Y, Sun J, Zhang R.	Curr Microbiol	10.1007/s00284-012-0299-9	2013
	The Performance of Ultrafiltration Process to Further Refine Lactic Acid from the Pre-Microfiltered Broth of Kitchen Waste Fermentation.	Guo Y, Li C, Zhao H, Wang X, Gao M, Sun X, Wang Q.	Membranes (Basel)	10.3390/membranes13030330	2023
Genetics	Complete genome sequence of Pelagibacterium halotolerans B2(T).	Huo YY, Cheng H, Han XF, Jiang XW, Sun C, Zhang XQ, Zhu XF, Liu YF, Li PF, Ni PX, Wu M.	J Bacteriol	10.1128/jb.06343-11	2012
Metabolism	A high-throughput screening strategy for nitrile-hydrolyzing enzymes based on ferric hydroxamate spectrophotometry.	He YC, Ma CL, Xu JH, Zhou L.	Appl Microbiol Biotechnol	10.1007/s00253-010-2977-5	2011
Metabolism	Aerobic Degradation of Clothianidin to 2-Chloro-methyl Thiazole and Methyl 3-(Thiazole-yl) Methyl Guanidine Produced by Pseudomonas stutzeri smk.	Parte SG, Kharat AS.	J Environ Public Health	10.1155/2019/4807913	2019
Enzymology	Characterization of a cold-active esterase from Serratia sp. and improvement of thermostability by directed evolution.	Jiang H, Zhang S, Gao H, Hu N.	BMC Biotechnol	10.1186/s12896-016-0235-3	2016
Phylogeny	Phylogenetic Co-Occurrence of ExoR, ExoS, and ChvI, Components of the RSI Bacterial Invasion Switch, Suggests a Key Adaptive Mechanism Regulating the Transition between Free-Living and Host-Invading Phases in Rhizobiales.	Heavner ME, Qiu WG, Cheng HP.	PLoS One	10.1371/journal.pone.0135655	2015
Metabolism	Biochemical characterization of a first fungal esterase from Rhizomucor miehei showing high efficiency of ester synthesis.	Liu Y, Xu H, Yan Q, Yang S, Duan X, Jiang Z.	PLoS One	10.1371/journal.pone.0077856	2013
	Halolysin R4 of Haloferax mediterranei confers its host antagonistic and defensive activities.	Chen S, Sun S, Wang R, Feng H, Xiang H.	Appl Environ Microbiol	10.1128/aem.02889-20	2021
	Pelagibacterium flavum sp. nov., Isolated from Soil Sample.	Chen XM, Yang ZZ, He SR, Xiong LS, Yuan Q, Zuo SY, Jiang CL, Jiang Y.	Curr Microbiol	10.1007/s00284-023-03583-8	2024
Phylogeny	Pelagibacterium lentulum sp. nov., a marine bacterium from the culture broth of Picochlorum sp. 122.	Wang G, Yu K, Wang Y, Su H, Wu H, Li T, Liang J, Huang W, Xiang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.002054	2017
Phylogeny	Pelagibacterium halotolerans gen. nov., sp. nov. and Pelagibacterium luteolum sp. nov., novel members of the family Hyphomicrobiaceae.	Xu XW, Huo YY, Wang CS, Oren A, Cui HL, Vedler E, Wu M	Int J Syst Evol Microbiol	10.1099/ijs.0.023325-0	2010

References

#16304	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22347
#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 )
#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) .
#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 )
#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 .
#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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Pelagibacterium halotolerans (DSM 22347, CGMCC 1.7692, JCM 15775)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000230555

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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