Name: Sulfuricaulis limicola HA5
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132366

Type strain:

Species: Sulfuricaulis limicola

Strain Designation: HA5

Culture col. no.: DSM 100373, NBRC 110752

Strain history: <- T. Watanabe, Univ. Hokkaido, Japan; HA5 <- H. Kojima; {2014}

NCBI tax ID(s): 1620215 (species)

SI-ID 401821

DSM 100373

Special Collections

Section

Sulfuricaulis limicola HA5 is an autotroph, mesophilic, Gram-negative bacterium that was isolated from sediment from a meromictic lake located in a residential area.

Gram-negative
motile
rod-shaped
autotroph
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Acidiferrobacterales*
	Family	*Acidiferrobacteraceae*
	Genus	*Sulfuricaulis*
	Species	**Sulfuricaulis limicola**
	Full Scientific Name (LPSN)	Sulfuricaulis limicola Kojima et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #65215]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.5

[Ref.: #65215]	Cell length	1.2-6.0 µm

[Ref.: #65215]	Cell width	0.3-0.5 µm

[Ref.: #65215]	Cell shape	rod-shaped

[Ref.: #65215]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24155]

Culture medium

SULFURIFUSTIS MEDIUM (DSMZ Medium 1277a)

[Ref.: #24155]

Culture medium growth

[Ref.: #24155]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24155]

Culture medium composition

expand / minimize

[Ref.: #65215]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #65215]

Culture medium growth

[Ref.: #65215]

Culture medium

[Ref.: #65215]

Culture medium growth

[Ref.: #65215]

Culture medium

LB (Luria-Bertani) MEDIUM

[Ref.: #65215]

Culture medium growth

[Ref.: #65215]

Culture medium

TSB

[Ref.: #65215]

Culture medium growth

		Temperature
[Ref.: #24155]	growth	28 °C
[Ref.: #65215]	growth	8-37 °C
[Ref.: #65215]	optimum	28-32 °C

	pH	Kind of pH		pH
[Ref.: #65215]			growth	6.1-9.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65215]

Nutrition type

autotroph

[Ref.: #69480]	Ability of spore formation	no Confidence in %90.112
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65215]		NaCl		optimum	0	M
[Ref.: #65215]		NaCl		growth	0-0.2	M

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65215]	elemental sulfur ChEBI	+	oxidation
[Ref.: #65215]	ferric oxide ChEBI	-	electron acceptor
[Ref.: #65215]	nitrate ChEBI	-	electron acceptor
[Ref.: #65215]	nitrite ChEBI	-	electron acceptor
[Ref.: #65215]	tetrathionate ChEBI	+	oxidation
[Ref.: #65215]	thiosulfate ChEBI	+	oxidation

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #65215]		catalase	-	1.11.1.6
[Ref.: #65215]		cytochrome oxidase	+	1.9.3.1

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65215]

Fatty acid	Percentage
C16:1ω7c and/or C16:1ω6c	45
C16:0	40.9
C10:0	6.2
iso-C17:1ω9c and/or C16:0 10-methyl	3
C18:1ω7c and/or C18:1ω6c	2.2
C10:0 3OH	1.4
C14:0	0.7
C17:0	0.4
C9:0	0.2

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	heme metabolism	92.86	13 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	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]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	purine metabolism	71.28	67 of 94
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	pyrimidine metabolism	53.33	24 of 45
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	propionate fermentation	50	5 of 10
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	oxidative phosphorylation	47.25	43 of 91
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	tryptophan metabolism	39.47	15 of 38
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	vitamin B12 metabolism	29.41	10 of 34
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	degradation of sugar acids	28	7 of 25
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		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.: #24155]	Sample type/isolated from	sediment from a meromictic lake located in a residential area
[Ref.: #24155]	Geographic location (country and/or sea, region)	Lake Harutori
[Ref.: #24155]	Country	Japan
[Ref.: #24155]	Country ISO 3 Code	JPN
[Ref.: #24155]	Continent	Asia

[Ref.: #65215]	Sample type/isolated from	sediment
[Ref.: #65215]	Geographic location (country and/or sea, region)	Lake Harutori
[Ref.: #65215]	Country	Japan
[Ref.: #65215]	Country ISO 3 Code	JPN
[Ref.: #65215]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC030205 (>99% sequence identity) for Sulfuricaulis limicola subclade from Microbeatlas

Aquatic Samples	4737
Soil Samples	3526
Animal Samples	359
Plant Samples	265
Total Samples	8887

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

[Ref.: #24155]

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.: #24155]	Sulfuricaulis limicola gene for 16S ribosomal RNA, partial sequence	LC030205	1453	GenBank ENA	1620215 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sulfuricaulis limicola HA5	GCA_002355735	complete	GenBank ENA	1620215 tax ID	*
[Ref.: #66792]	Sulfuricaulis limicola HA5	2775506817	complete	JGI IMG/M	1620215 tax ID	*

[Ref.: #24155]	GC-content	63 mol%	high performance liquid chromatography (HPLC)
[Ref.: #24155]	GC-content	61.4 mol%	sequence analysis

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Sulfuricaulis limicola HA5 NCBI: GCA_002355735.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sulfuricaulis limicola HA5 NCBI: GCA_002355735.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.5	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	82.557	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	56.242	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	90.112	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	85.828	no
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	50.471	no

Availability in culture collections External links

[Ref.: #24155]

Culture collection no.

DSM 100373, NBRC 110752

[Ref.: #90712]

SI-ID 401821

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sulfuricaulis limicola gen. nov., sp. nov., a sulfur oxidizer isolated from a lake.	Kojima H, Watanabe T, Fukui M	Int J Syst Evol Microbiol	10.1099/ijsem.0.000709	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 )

#24155

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100373

#65215

Hisaya Kojima, Tomohiro Watanabe, Manabu Fukui: Sulfuricaulis limicola gen. nov., sp. nov., a sulfur oxidizer isolated from a lake. IJSEM 66: 266 - 270 2016 ( DOI 10.1099/ijsem.0.000709 , PubMed 26503693 )

#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 )

#90712

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-ID401821.1 )

* These data were automatically processed and therefore are not curated

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