Name: Bermanella marisrubri RED65
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11297

Type strain:

Species: Bermanella marisrubri

Strain Designation: RED65

Culture col. no.: DSM 23232, CCUG 52064, CECT 7074

Strain history: <- CECT <- J. Pinhassi, Dept. Biology and Environmental Sci., Univ. Kalmar, Sweden

NCBI tax ID(s): 207949 (species)

SI-ID 360707

CCUG 52064, CECT 7074, DSM 23232

Section

Bermanella marisrubri RED65 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface-seawater sample.

Gram-negative
motile
spiral-shaped
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Oceanospirillales*
	Family	*Oceanospirillaceae*
	Genus	*Bermanella*
	Species	**Bermanella marisrubri**
	Full Scientific Name (LPSN)	Bermanella marisrubri Pinhassi et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #28937]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #28937]	Cell length	3.15 µm

[Ref.: #28937]	Cell width	0.45 µm

[Ref.: #28937]	Cell shape	spiral-shaped

[Ref.: #28937]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %95.504

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16761]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)

[Ref.: #16761]

Culture medium growth

[Ref.: #16761]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16761]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16761]	growth	28 °C
[Ref.: #28937]	growth	15-42 °C
[Ref.: #28937]	optimum	27.5 °C
[Ref.: #59417]	growth	25 °C

[Ref.: #16761]	Temperature range	mesophilic
[Ref.: #28937]	Temperature range	mesophilic
[Ref.: #59417]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28937]	Oxygen tolerance	aerobe
[Ref.: #59417]	Oxygen tolerance	aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28937]		NaCl		growth	01-12	%
[Ref.: #28937]		NaCl		optimum	6.5	%

[Ref.: #28937]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28937]	acetate ChEBI	+	carbon source
[Ref.: #28937]	glutamate ChEBI	+	carbon source
[Ref.: #28937]	malate ChEBI	+	carbon source
[Ref.: #28937]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #28937]	succinate ChEBI	+	carbon source
[Ref.: #28937]	tween 40 ChEBI	+	carbon source
[Ref.: #28937]	tween 80 ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #28937]		catalase	+	1.11.1.6
[Ref.: #28937]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	lipid A biosynthesis	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	polyamine pathway	65.22	15 of 23
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	allantoin degradation	55.56	5 of 9
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	glycolysis	52.94	9 of 17
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	oxidative phosphorylation	43.96	40 of 91
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	vitamin B12 metabolism	26.47	9 of 34
[Ref.: #66794]	glycogen biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	degradation of hexoses	22.22	4 of 18
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #16761]	Sample type/isolated from	surface-seawater sample
[Ref.: #16761]	Geographic location (country and/or sea, region)	northern Red Sea, Gulf of Eilat
[Ref.: #16761]	Country	Israel
[Ref.: #16761]	Country ISO 3 Code	ISR
[Ref.: #16761]	Continent	Asia

[Ref.: #59417]	Sample type/isolated from	Seawater surface
[Ref.: #59417]	Sampling date	2000-09-24
[Ref.: #59417]	Geographic location (country and/or sea, region)	Red Sea,Gulf of Eilat
[Ref.: #59417]	Country	Israel
[Ref.: #59417]	Country ISO 3 Code	ISR
[Ref.: #59417]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY136131 (>99% sequence identity) for Bermanella marisrubri subclade from Microbeatlas

Aquatic Samples	4489
Soil Samples	203
Animal Samples	405
Plant Samples	75
Total Samples	5172

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #16761]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #16761]	Bermanella marisrubri strain RED65 16S ribosomal RNA gene, complete sequence	AY136131	1533	ENA	207949 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Bermanella marisrubri RED65	GCA_012295615	complete	GenBank	207949 tax ID	*
[Ref.: #66792]	Bermanella marisrubri RED65	GCA_000153565	scaffold	GenBank	207949 tax ID	*
[Ref.: #66792]	Bermanella marisrubri RED65	638341141	draft	JGI IMG/M	207949 tax ID	*

[Ref.: #16761]	GC-content	44.0 mol%
[Ref.: #28937]	GC-content	44 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Bermanella marisrubri RED65 NCBI: GCA_012295615.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bermanella marisrubri RED65 NCBI: GCA_012295615.1
[Ref.: #69480]	motile	yes	92.215	yes
[Ref.: #69480]	flagellated	yes	92.278	no
[Ref.: #69480]	gram-positive	no	98.928	yes
[Ref.: #69480]	anaerobic	no	98.608	yes
[Ref.: #69480]	aerobic	yes	94.028	no
[Ref.: #69480]	halophile	yes	90.095	yes
[Ref.: #69480]	spore-forming	no	95.681	no
[Ref.: #69480]	glucose-util	yes	60.268	no
[Ref.: #69480]	thermophile	no	99.277	yes
[Ref.: #69480]	glucose-ferment	no	87.437	no

Availability in culture collections External links

[Ref.: #16761]

Culture collection no.

DSM 23232, CCUG 52064, CECT 7074

[Ref.: #80530]

SI-ID 360707

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	A novel bacterial enzyme with D-glucuronyl C5-epimerase activity.	Raedts J, Lundgren M, Kengen SW, Li JP, van der Oost J	J Biol Chem	10.1074/jbc.M113.476440	2013	*
Phylogeny	Bermanella marisrubri gen. nov., sp. nov., a genome-sequenced gammaproteobacterium from the Red Sea.	Pinhassi J, Pujalte MJ, Pascual J, Gonzalez JM, Lekunberri I, Pedros-Alio C, Arahal DR	Int J Syst Evol Microbiol	10.1099/ijs.0.002113-0	2009	*

References

#16761

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23232

#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 )

#28937

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 #25376 (see below)

#59417 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52064

#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 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#80530

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID360707.1 )

#25376

IJSEM 373 2009 ( DOI 10.1099/ijs.0.002113-0 , PubMed 19196781 )

* These data were automatically processed and therefore are not curated

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