Methylophaga thalassica (DSM 5690, ATCC 33146, IAM 12458)

Name: Methylophaga thalassica (DSM 5690, ATCC 33146, IAM 12458)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11904

Type strain

Culture col. no. DSM 5690 ATCC 33146 IAM 12458 LMG 4055 NCIMB 2163 5 more

NCBI tax ID(s) 40223

Special Collections DSMZ JCM KCTC CIP

Links

Methylophaga thalassica DSM 5690 is a mesophilic prokaryote that was isolated from seawater.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 3573

LMG 4055,ATCC 33146,IAM 12458,NCMB 2163,CIP 104552,JCM 6887,NCIMB 2163,DSM 5690,VKM B-2057,KCTC 2861,NBRC 102424

@ref 20215

Last LPSN update 2025-12-16 09:49:43

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Beggiatoales

Family Piscirickettsiaceae

Genus Methylophaga

Species Methylophaga thalassica

Full scientific name Methylophaga thalassica Janvier et al. 1985

BacDive ID	Other strains from **Methylophaga thalassica** (6)	Type strain
137734	M. thalassica CIP 104726, ATCC 33145, IAM 12457, NCIMB ...
138075	M. thalassica CIP 104563, LMG 2878, NCIMB 2160
138076	M. thalassica 150, CIP 104564
138077	M. thalassica 1d, CIP 104565
138380	M. thalassica FERMP-3622, CIP 106896, NCIMB 2162, FERM ...
157950	M. thalassica DSM 9438, FERM P-4515, IAM 12459, LMG 2877, ...

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
2287	MEDIUM FOR MARINE METHYLOTROPHS (DSMZ Medium 750)	Medium recipe at MediaDive	Name: MEDIUM FOR MARINE METHYLOTROPHS (DSMZ Medium 750) Composition: NaCl 25.0 g/l Agar 20.0 g/l Peptone 10.0 g/l Methanol 7.92 g/l Beef extract 7.0 g/l (NH4)2SO4 1.0 g/l K2HPO4 1.0 g/l Distilled water
39039	MEDIUM 138 - for Methylophaga thalassica and Methylophaga marina		Distilled water make up to (972.000 ml);Sodium chloride (24.000 g);Potassium chloride (0.500 g);Magnesium chloride hexahydrate (3.000 g);Magnesium sulphate heptahydrate (2.000 g);Calcium chloride dihydrate (1.000 g);Methanol (6.000 ml);Trizma hydrochlorid
123498	CIP Medium 138	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2287	positive	growth	25-30	mesophilic
39039	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Observation

67770

Observationquinones: Q-8

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
2287	seawater	Kanagawa Prefecture	Japan	JPN	Asia
67770	Coastal seawater	Kanagawa	Japan	JPN	Asia
123498	Environment, Coastal sea water	Kanagawa	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence X87339 (>99% sequence identity) for Methylophaga thalassica from Microbeatlas

Aquatic Samples	189
Soil Samples	9
Animal Samples	14
Plant Samples
Total Samples	212

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2287	1	Risk group (German classification) According to TRBA 466
123498	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
124043	ASM3015979v1 assembly for Methylophaga thalassica NBRC 102424	contig	GCA_030159795	40223.6	8108158397	40223	75.62
124043	ASM4266168v1 assembly for Methylophaga thalassica NBRC 102424	contig	GCA_042661685			40223	68.28

Genome browser: GCA_030159795

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	M.thalassica DNA for 16S ribosomal RNA (ATCC 33146)	X87339	1489	40223
20218	M.thalassica mRNA for 16S ribosomal RNA	X95460	1491	40223
20218	Methylophaga thalassica gene for 16S rRNA, partial sequence, strain: NBRC 102424	AB681780	1463	40223

GC content

@ref	GC-content (mol%)	Method
67770	44.9	high performance liquid chromatography (HPLC)
67770	44	thermal denaturation, midpoint method (Tm)
67770	43.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenetic profiling of bacterial community from two intimately located sites in Balramgari, North-East coast of India.	Gupta AK, Rangrez AY, Verma P, Chatterji A, Shouche YS.	Indian J Microbiol	10.1007/s12088-009-0034-9	2009
	Lignin Unlocks Stealth Carbon Sinks in Cold Seeps via Microbial Enzymatic Gatekeeping.	Li J, Feng J, Wang P, Zhu M, Huang Y, Wu Y, Fan J, Hu J, Dong X, Zhou Y, Tao X, Zhang S.	Research (Wash D C)	10.34133/research.0848	2025
Metabolism	Role of EctR as transcriptional regulator of ectoine biosynthesis genes in Methylophaga thalassica.	Mustakhimov II, Reshetnikov AS, Fedorov DN, Khmelenina VN, Trotsenko YA.	Biochemistry (Mosc)	10.1134/s0006297912080068	2012
Phylogeny	Emended description of the genus Methylophaga Janvier et al. 1985.	Boden R.	Int J Syst Evol Microbiol	10.1099/ijs.0.033639-0	2012
Phylogeny	Diversity and phylogeny of the ectoine biosynthesis genes in aerobic, moderately halophilic methylotrophic bacteria.	Reshetnikov AS, Khmelenina VN, Mustakhimov II, Kalyuzhnaya M, Lidstrom M, Trotsenko YA.	Extremophiles	10.1007/s00792-011-0396-x	2011
Metabolism	[Biosynthesis of the bioprotectant ectoin by aerobic methylotrophic bacteria from methanol].	Doronina NV, Ezhov VA, Beschastnyi AP, Trotsenko IuA.	Prikl Biokhim Mikrobiol	10.1134/s0003683810020080	2010
Enzymology	Genes and enzymes of ectoine biosynthesis in halotolerant methanotrophs.	Reshetnikov AS, Khmelenina VN, Mustakhimov II, Trotsenko YA.	Methods Enzymol	10.1016/b978-0-12-386905-0.00002-4	2011
Genetics	Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia.	Moh TH, Lau NS, Furusawa G, Amirul AA.	Stand Genomic Sci	10.1186/s40793-017-0248-0	2017
Metabolism	GlnR-Mediated Regulation of ectABCD Transcription Expands the Role of the GlnR Regulon to Osmotic Stress Management.	Shao Z, Deng W, Li S, He J, Ren S, Huang W, Lu Y, Zhao G, Cai Z, Wang J.	J Bacteriol	10.1128/jb.00185-15	2015
	CosR Is a Global Regulator of the Osmotic Stress Response with Widespread Distribution among Bacteria.	Gregory GJ, Morreale DP, Boyd EF.	Appl Environ Microbiol	10.1128/aem.00120-20	2020
Metabolism	A Gcn5-Related N-Acetyltransferase (GNAT) Capable of Acetylating Polymyxin B and Colistin Antibiotics in Vitro.	Czub MP, Zhang B, Chiarelli MP, Majorek KA, Joe L, Porebski PJ, Revilla A, Wu W, Becker DP, Minor W, Kuhn ML.	Biochemistry	10.1021/acs.biochem.8b00946	2018
	The architecture of the diaminobutyrate acetyltransferase active site provides mechanistic insight into the biosynthesis of the chemical chaperone ectoine.	Richter AA, Kobus S, Czech L, Hoeppner A, Zarzycki J, Erb TJ, Lauterbach L, Dickschat JS, Bremer E, Smits SHJ.	J Biol Chem	10.1074/jbc.ra119.011277	2020
Enzymology	Characterization of the recombinant diaminobutyric acid acetyltransferase from Methylophaga thalassica and Methylophaga alcalica.	Mustakhimov II, Rozova ON, Reshetnikov AS, Khmelenina VN, Murrell JC, Trotsenko YA	FEMS Microbiol Lett	10.1111/j.1574-6968.2008.01156.x	2008

References

#2287	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5690
#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 )
#39039	; Curators of the CIP;
#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 .
#123498	Collection of Institut Pasteur ; Curators of the CIP; CIP 104552
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Methylophaga thalassica (DSM 5690, ATCC 33146, IAM 12458)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_030159795

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

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