Name: Serpentinicella alkaliphila 3b
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132680

Type strain:

Species: Serpentinicella alkaliphila

Strain Designation: 3b

Culture col. no.: DSM 100013, JCM 30645

Strain history: M. Quemeneur; Mediterr. Inst. of Oceanogr., France; 3b.

NCBI tax ID(s): 1734049 (species)

SI-ID 406320

DSM 100013

Section

Serpentinicella alkaliphila 3b is an obligate anaerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from hyperalkaline spring in a serpentinite-hosted hydrothermal field, carbonate chimney.

colony-forming
Gram-positive
motile
rod-shaped
spore-forming
obligate anaerobe
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Clostridiaceae*
	Genus	*Serpentinicella*
	Species	**Serpentinicella alkaliphila**
	Full Scientific Name (LPSN)	Serpentinicella alkaliphila Mei et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #25025]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #25025]	Cell length	1.0-10.0 µm

[Ref.: #25025]	Cell width	0.4-0.6 µm

[Ref.: #25025]	Cell shape	rod-shaped

[Ref.: #25025]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %96.227

[Ref.: #25025]	Colony size	1.0-2.0 mm
[Ref.: #25025]	Colony color	yellow
[Ref.: #25025]	Colony shape	circular
[Ref.: #25025]	Incubation period	7 days
[Ref.: #25025]	Cultivation medium used	BYG medium

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25025]

Culture medium

BYG medium

[Ref.: #25025]

Culture medium growth

[Ref.: #24469]

Culture medium

SERPENTINICELLA MEDIUM (DSMZ Medium 898b)

[Ref.: #24469]

Culture medium growth

[Ref.: #24469]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24469]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24469]	growth	37 °C
[Ref.: #25025]	growth	30-43 °C
[Ref.: #25025]	optimum	37 °C
[Ref.: #67770]	growth	35 °C

[Ref.: #24469]	Temperature range	mesophilic
[Ref.: #25025]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25025]			optimum	9.5
[Ref.: #25025]			growth	7.8-10.1

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25025]	Oxygen tolerance	obligate anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.714

[Ref.: #25025]	Spore description	terminal without swollen sporangia, 0.5–0.7 µm in diameter
[Ref.: #25025]	Type of spore	spore
[Ref.: #25025]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25025]		NaCl		growth	0-4.0	%(w/v)
[Ref.: #25025]		NaCl		optimum	0-0.2	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25025]	acetoacetate ChEBI	-	electron donor
[Ref.: #25025]	arabinose ChEBI	-	electron donor
[Ref.: #25025]	arsenate ChEBI	-	electron acceptor
[Ref.: #25025]	casamino acids	-	electron donor
[Ref.: #25025]	cellobiose ChEBI	-	electron donor
[Ref.: #25025]	chromate ChEBI	-	electron acceptor
[Ref.: #25025]	crotonate ChEBI	+	electron donor
[Ref.: #25025]	dimethyl sulfoxide ChEBI	-	electron acceptor
[Ref.: #25025]	elemental sulfur ChEBI	-	electron acceptor
[Ref.: #25025]	ethanol ChEBI	-	electron donor
[Ref.: #25025]	ethylenediaminetetraacetatoferrate ChEBI	-	electron acceptor
[Ref.: #25025]	ferric citrate ChEBI	-	electron acceptor
[Ref.: #25025]	ferric iron ChEBI	-	electron acceptor
[Ref.: #25025]	formate ChEBI	-	electron donor
[Ref.: #25025]	fructose ChEBI	-	electron donor
[Ref.: #25025]	fumarate ChEBI	-	electron donor
[Ref.: #25025]	fumarate ChEBI	+	electron acceptor
[Ref.: #25025]	galactose ChEBI	-	electron donor
[Ref.: #25025]	glucose ChEBI	-	electron donor
[Ref.: #25025]	glycerol ChEBI	-	electron donor
[Ref.: #25025]	iron trichloride ChEBI	-	electron acceptor
[Ref.: #25025]	lactate ChEBI	+	electron donor
[Ref.: #25025]	lactose ChEBI	-	electron donor
[Ref.: #25025]	maltose ChEBI	-	electron donor
[Ref.: #25025]	mannose ChEBI	-	electron donor
[Ref.: #25025]	nitrate ChEBI	-	electron acceptor
[Ref.: #25025]	nitrite ChEBI	-	electron acceptor
[Ref.: #25025]	peptone	-	electron donor
[Ref.: #25025]	pyruvate ChEBI	+	electron donor
[Ref.: #25025]	raffinose ChEBI	-	electron donor
[Ref.: #25025]	rhamnose ChEBI	-	electron donor
[Ref.: #25025]	ribose ChEBI	-	electron donor
[Ref.: #25025]	selenite ChEBI	-	electron acceptor
[Ref.: #25025]	sodium chloride ChEBI	-	required for growth
[Ref.: #25025]	sucrose ChEBI	-	electron donor
[Ref.: #25025]	sulfate ChEBI	-	electron acceptor
[Ref.: #25025]	sulfite ChEBI	-	electron acceptor
[Ref.: #25025]	thiosulfate ChEBI	-	electron acceptor
[Ref.: #25025]	xylose ChEBI	-	electron donor
[Ref.: #25025]	yeast extract	+	required for growth
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	pyrimidine metabolism	86.67	39 of 45
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	vitamin B12 metabolism	85.29	29 of 34
[Ref.: #66794]	glycolate and glyoxylate degradation	83.33	5 of 6
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	chorismate metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	phenylalanine metabolism	53.85	7 of 13
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	oxidative phosphorylation	51.65	47 of 91
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	starch degradation	50	5 of 10
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	lipid metabolism	48.39	15 of 31
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	non-pathway related	47.37	18 of 38
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	degradation of sugar acids	40	10 of 25
[Ref.: #66794]	flavin biosynthesis	40	6 of 15
[Ref.: #66794]	isoprenoid biosynthesis	38.46	10 of 26
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	35.29	6 of 17
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
		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.: #24469]	Sample type/isolated from	hyperalkaline spring in a serpentinite-hosted hydrothermal field, carbonate chimney
[Ref.: #24469]	Geographic location (country and/or sea, region)	New Caledonia, Prony Bay, Rivière des Kaoris
[Ref.: #24469]	Country	France
[Ref.: #24469]	Country ISO 3 Code	FRA
[Ref.: #24469]	Continent	Europe
[Ref.: #24469]	Geographic location	-22.2995°/166.8620°

[Ref.: #67770]	Sample type/isolated from	Carbonaceous hydrothermal chimney in Prony Bay
[Ref.: #67770]	Geographic location (country and/or sea, region)	New Caledonia
[Ref.: #67770]	Country	French Overseas
[Ref.: #67770]	Country ISO 3 Code	FRA
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Thermal spring
#Condition	#Alkaline	-
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KR349722 (>99% sequence identity) for Serpentinicella alkaliphila subclade from Microbeatlas

Aquatic Samples	55
Soil Samples	9
Animal Samples	2
Plant Samples	4
Total Samples	70

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

[Ref.: #24469]

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.: #24469]	Serpentinicella alkaliphila strain 3b 16S ribosomal RNA gene, partial sequence	KR349722	1417	ENA	1734049 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Serpentinicella alkaliphila DSM 100013	GCA_004345905	scaffold	GenBank	1734049 tax ID
[Ref.: #66792]	Serpentinicella alkaliphila 3B	GCA_018141405	chromosome	GenBank	1734049 tax ID	*
[Ref.: #66792]	Serpentinicella alkaliphila strain DSM 100013	1734049.3	wgs	PATRIC	1734049 tax ID	*
[Ref.: #66792]	Serpentinicella alkaliphila DSM 100013	2795386145	draft	JGI IMG/M	1734049 tax ID	*

[Ref.: #24469]

GC-content

33.2 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: Serpentinicella alkaliphila strain DSM 100013 PATRIC: 1734049.4
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Serpentinicella alkaliphila 3B NCBI: GCA_018141405.1
[Ref.: #69480]	flagellated	yes	50.946	no
[Ref.: #69480]	gram-positive	no	62.773	no
[Ref.: #69480]	anaerobic	yes	98.999	yes
[Ref.: #69480]	aerobic	no	97.787	yes
[Ref.: #69480]	halophile	no	87.316	no
[Ref.: #69480]	spore-forming	yes	95.846	yes
[Ref.: #69480]	thermophile	no	97.273	yes
[Ref.: #69480]	glucose-util	yes	82.9	no
[Ref.: #69480]	motile	yes	87.25	yes
[Ref.: #69480]	glucose-ferment	no	68.072	no

Availability in culture collections External links

[Ref.: #24469]

Culture collection no.

DSM 100013, JCM 30645

[Ref.: #90988]

SI-ID 406320

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Serpentinicella alkaliphila gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from the serpentinite-hosted Prony hydrothermal field, New Caledonia.	Mei N, Postec A, Erauso G, Joseph M, Pelletier B, Payri C, Ollivier B, Quemeneur M	Int J Syst Evol Microbiol	10.1099/ijsem.0.001375	2016	*

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 )

#24469

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100013

#25025

N. P. Mei, A.,Erauso, G.,Joseph, M.,Pelletier, B.,Payri, C.,Ollivier, B.,Quéméneur, M.: Serpentinicella alkaliphila gen. nov., sp. nov., a novel alkaliphilic anaerobic bacterium isolated from the serpentinite-hosted Prony hydrothermal field, New Caledonia. IJSEM 66: 4464 - 4470 2016 ( DOI 10.1099/ijsem.0.001375 , PubMed 27499124 )

#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 )

#90988

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-ID406320.1 )

* These data were automatically processed and therefore are not curated

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Serpentinicella alkaliphila strain DSM 100013

Serpentinicella alkaliphila 3B

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