Methylobrevis pamukkalensis (DSM 29599, JCM 30229, VKM B-2849)

Name: Methylobrevis pamukkalensis (DSM 29599, JCM 30229, VKM B-2849)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140090

Type strain

Strain Designation PK2

Culture col. no. DSM 29599 JCM 30229 VKM B-2849 CCUG 65431 PK2

NCBI tax ID(s) 1439726

Special Collections DSMZ CCUG JCM

History DSMZ <- N. V. Doronina, Inst. Biochem. Physiol. Microorg., RAS, Pushchino, Russia; PK2 JCM <-- N. V. Doronina; G. K. Skryabin Inst. of Biochem. & Physiol. of Microorg., RAS, Russia; PK2.

Links

Methylobrevis pamukkalensis PK2 is an aerobe bacterium that was isolated from water of a saline hotspring.

aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397290

JCM 30229,VKM B-2849,DSM 29599

@ref 20215

Last LPSN update 2026-05-29 08:39:38

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Pleomorphomonadaceae

Genus Methylobrevis

Species Methylobrevis pamukkalensis

Full scientific name Methylobrevis pamukkalensis Poroshina et al. 2015

Morphology

Colony morphology

63223

Incubation period5 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
42697	MEDIUM K (DSMZ Medium 1122)		Medium recipe at MediaDive	Name: MEDIUM K (DSMZ Medium 1122) Composition: Agar 20.0 g/l KH2PO4 2.0 g/l (NH4)2SO4 2.0 g/l NaCl 0.5 g/l MgSO4 x 7 H2O 0.125 g/l FeSO4 x 7 H2O 0.002 g/l Methanol Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
42697	positive	growth	28
63223	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
63223	aerobe
125439	obligate aerobe	98.073

Spore formation

@ref	Spore formation	Confidence
125439		94.93

Observation

67770

Observationquinones: Q-10

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ppGpp biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	methylglyoxal degradation	100	5 of 5
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	glycogen metabolism	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	formaldehyde oxidation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	suberin monomers biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	valine metabolism	100	9 of 9
66794	folate polyglutamylation	100	1 of 1
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	cardiolipin biosynthesis	100	7 of 7
66794	photosynthesis	92.86	13 of 14
66794	degradation of aromatic, nitrogen containing compounds	91.67	11 of 12
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	lipid A biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	phenylalanine metabolism	84.62	11 of 13
66794	alanine metabolism	82.76	24 of 29
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	3-chlorocatechol degradation	80	4 of 5
66794	methanofuran biosynthesis	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	histidine metabolism	79.31	23 of 29
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	allantoin degradation	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	biotin biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	degradation of pentoses	75	21 of 28
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	glycogen biosynthesis	75	3 of 4
66794	proline metabolism	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	pyrimidine metabolism	71.11	32 of 45
66794	arginine metabolism	70.83	17 of 24
66794	propionate fermentation	70	7 of 10
66794	starch degradation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	leucine metabolism	69.23	9 of 13
66794	non-pathway related	68.42	26 of 38
66794	oxidative phosphorylation	68.13	62 of 91
66794	lipid metabolism	67.74	21 of 31
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	cyanate degradation	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	glycolysis	64.71	11 of 17
66794	citric acid cycle	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	lysine metabolism	61.9	26 of 42
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	myo-inositol biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	methanogenesis from CO2	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	polyamine pathway	56.52	13 of 23
66794	cysteine metabolism	55.56	10 of 18
66794	d-mannose degradation	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	cyclohexanol degradation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	tyrosine metabolism	50	7 of 14
66794	phenylmercury acetate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	phenol degradation	45	9 of 20
66794	degradation of sugar acids	44	11 of 25
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	gallate degradation	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	D-cycloserine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	chlorophyll metabolism	38.89	7 of 18
66794	arachidonic acid metabolism	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	carotenoid biosynthesis	36.36	8 of 22
66794	d-xylose degradation	36.36	4 of 11
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	sulfate reduction	30.77	4 of 13
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	nitrate assimilation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Condition	#Saline	-
#Condition	#Thermophilic (>45°C)	-
#Environmental	#Aquatic	#Thermal spring

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
42697	water of a saline hotspring		Denizli, Hierapolis, Pamukkale	Turkey	TUR	Asia
63223	Saline water	2011-10-15	Pamukkale	Turkey	TUR	Asia
67770	Saline hot spring of the Pamukkale		Hierapolis, Denizli	Turkey	TUR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KF683074 (>99% sequence identity) for Methylobrevis pamukkalensis subclade from Microbeatlas

Aquatic Samples	337
Soil Samples	403
Animal Samples	299
Plant Samples	79
Total Samples	1118

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
42697	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	MpPK2_01 assembly for Methylobrevis pamukkalensis PK2	contig	GCA_001720135	1439726.6	2786546839	1439726	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
42697	Methylobrevis pamukkalensis strain PK2 16S ribosomal RNA gene, partial sequence	KF683074	1367		1439726

GC content

@ref	GC-content (mol%)	Method
42697	67.9	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: MpPK2_01 assembly for Methylobrevis pamukkalensis PK2
NCBI: GCA_001720135

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	58.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.07	no
125439	motility	BacteriaNetⓘ	yes	55.43	no
125439	spore_formation	BacteriaNetⓘ	no	94.93	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	From genome to evolution: investigating type II methylotrophs using a pangenomic analysis.	Samanta D, Rauniyar S, Saxena P, Sani RK.	mSystems	10.1128/msystems.00248-24	2024
	Refining the taxonomy of the order Hyphomicrobiales (Rhizobiales) based on whole genome comparisons of over 130 type strains.	diCenzo GC, Yang Y, Young JPW, Kuzmanovic N.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006328	2024
Genetics	Sequencing and de novo assembly of the Koshihikari genome and identification of the genomic region related to the eating quality of cooked rice.	Lee YK, Lee Y, Jang S, Lee T, Woo MO, Seo J, Kim B, Koh HJ.	Mol Breed	10.1007/s11032-022-01335-3	2022
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Phylogeny	Methylobrevis albus sp. nov., isolated from freshwater lake sediment.	Zou QH, Feng X, Wang TJ, Du ZJ	Arch Microbiol	10.1007/s00203-021-02442-z	2021
Phylogeny	Methylobrevis pamukkalensis gen. nov., sp. nov., a halotolerant restricted facultative methylotroph isolated from saline water.	Poroshina MN, Trotsenko YA, Doronina NV	Int J Syst Evol Microbiol	10.1099/ijs.0.000105	2015

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 )
#42697	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29599
#63223	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 65431
#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 .
#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 )

Content

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Methylobrevis pamukkalensis (DSM 29599, JCM 30229, VKM B-2849)

Name and taxonomic classification

Morphology

Colony 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_001720135

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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