Name: Rhodobacter maris JA276
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 134339

Type strain:

Species: Rhodobacter maris

Strain Designation: JA276

Culture col. no.: JCM 14794, ATCC BAA-1549, CCUG 55129

Strain history: Ch. Sasikala JA276.

NCBI tax ID(s): 446682 (species)

SI-ID 410440

CCUG 55129

Section

Rhodobacter maris JA276 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from marine sediment.

Gram-negative
ovoid-shaped
facultative anaerobe
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	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Rhodobacter*
	Species	**Rhodobacter maris**
	Full Scientific Name (LPSN)	Rhodobacter maris Venkata Ramana et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32530]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #32530]	Cell length	1-1.5 µm

[Ref.: #32530]	Cell width	0.6-1 µm

[Ref.: #32530]	Cell shape	ovoid-shaped

[Ref.: #32530]	Motility	no

[Ref.: #32530]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #32530]	growth	25-35 °C
[Ref.: #32530]	optimum	30 °C
[Ref.: #60470]	growth	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #32530]	Temperature range	mesophilic
[Ref.: #60470]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32530]			optimum	6.5-7
[Ref.: #32530]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32530]	Oxygen tolerance	facultative anaerobe
[Ref.: #60470]	Oxygen tolerance	aerobe

[Ref.: #32530]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32530]		NaCl		growth	0-3	%
[Ref.: #32530]		NaCl		optimum	0-3	%

[Ref.: #32530]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32530]	acetate ChEBI	+	carbon source
[Ref.: #32530]	glycerol ChEBI	+	carbon source
[Ref.: #32530]	lactate ChEBI	+	carbon source
[Ref.: #32530]	malate ChEBI	+	carbon source
[Ref.: #32530]	pyruvate ChEBI	+	carbon source
[Ref.: #32530]	valerate ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	allantoin degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	purine metabolism	86.17	81 of 94
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	84.44	38 of 45
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	chlorophyll metabolism	72.22	13 of 18
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	lysine metabolism	69.05	29 of 42
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	arginine metabolism	66.67	16 of 24
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	alginate biosynthesis	50	2 of 4
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	carotenoid biosynthesis	36.36	8 of 22
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin 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]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #32530]	Sample type/isolated from	marine sediment

[Ref.: #60470]	Sample type/isolated from	Mud from fishing area,sea shore
[Ref.: #60470]	Sampling date	2006-12-28
[Ref.: #60470]	Geographic location (country and/or sea, region)	Cochin,Kerala
[Ref.: #60470]	Country	India
[Ref.: #60470]	Country ISO 3 Code	IND
[Ref.: #60470]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Samples of a sediment collected from the seashore of Cochin
[Ref.: #67770]	Geographic location (country and/or sea, region)	Kerala State
[Ref.: #67770]	Country	India
[Ref.: #67770]	Country ISO 3 Code	IND
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM745438 (>99% sequence identity) for Rhodobacter maris subclade from Microbeatlas

Aquatic Samples	311
Soil Samples	16
Animal Samples	37
Plant Samples	15
Total Samples	379

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.: #32530]	Rhodobacter maris partial 16S rRNA gene, type strain JA276	AM745438	1377	GenBank	446682 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodobacter maris JA276	GCA_900217815	scaffold	GenBank	446682 tax ID	*
[Ref.: #66792]	Rhodobacter maris JA276	2739368070	draft	JGI IMG/M	446682 tax ID	*

[Ref.: #32530]	GC-content	62.85 mol%
[Ref.: #67770]	GC-content	62.85 mol%	high performance liquid chromatography (HPLC)

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: Rhodobacter maris JA276 NCBI: GCA_900217815.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodobacter maris JA276 NCBI: GCA_900217815.1
[Ref.: #69480]	flagellated	no	81.053	yes
[Ref.: #69480]	gram-positive	no	98.839	yes
[Ref.: #69480]	anaerobic	no	82.626	yes
[Ref.: #69480]	aerobic	no	93.328	no
[Ref.: #69480]	halophile	no	86.311	no
[Ref.: #69480]	spore-forming	no	95.439	yes
[Ref.: #69480]	thermophile	no	94.748	no
[Ref.: #69480]	glucose-util	yes	79.748	no
[Ref.: #69480]	motile	yes	55.734	yes
[Ref.: #69480]	glucose-ferment	no	87.764	no

Availability in culture collections External links

[Ref.: #32530]

Culture collection no.

JCM 14794, ATCC BAA-1549, CCUG 55129

[Ref.: #91903]

SI-ID 410440

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of Rhodobacter azollae sp. nov. and Rhodobacter lacus sp. nov.	Suresh G, Sailaja B, Ashif A, Dave BP, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijsem.0.002107	2017	*
Phylogeny	Paenirhodobacter enshiensis gen. nov., sp. nov., a non-photosynthetic bacterium isolated from soil, and emended descriptions of the genera Rhodobacter and Haematobacter.	Wang D, Liu H, Zheng S, Wang G	Int J Syst Evol Microbiol	10.1099/ijs.0.050351-0	2013	*
Phylogeny	Rhodobacter viridis sp. nov., a phototrophic bacterium isolated from mud of a stream.	Raj PS, Ramaprasad EVV, Vaseef S, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.038471-0	2012	*
Phylogeny	Rhodobacter maris sp. nov., a phototrophic alphaproteobacterium isolated from a marine habitat of India.	Venkata Ramana V, Sasikala Ch, Ramana ChV	Int J Syst Evol Microbiol	10.1099/ijs.0.65638-0	2008	*

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 )

#32530

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 #28748 (see below)

#60470 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55129

#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 .

#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 )

#91903

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-ID410440.1 )

#28748

IJSEM 1719 2008 ( DOI 10.1099/ijs.0.65638-0 , PubMed 18599723 )

* These data were automatically processed and therefore are not curated

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