Name: Nitrincola lacisaponensis 4CA
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11284

Type strain:

Species: Nitrincola lacisaponensis

Strain Designation: 4CA

Culture col. no.: DSM 16316, ATCC BAA-920

Strain history: <- P. A. Dimitriu, Dept. Biolog. Sci., Univ. Missouri-Rolla, USA; 4CA

NCBI tax ID(s): 267850 (species)

SI-ID 405043

DSM 16316

Section

Nitrincola lacisaponensis 4CA is an aerobe, mesophilic, Gram-negative bacterium that was isolated from decomposing wood taken from the shore of Soap Lake, a meromictic, saline, alkaline lake.

Gram-negative
motile
rod-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	*Nitrincola*
	Species	**Nitrincola lacisaponensis**
	Full Scientific Name (LPSN)	Nitrincola lacisaponensis Dimitriu et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #31482]	Gram stain	negative

[Ref.: #31482]	Cell length	1.4 µm

[Ref.: #31482]	Cell width	0.5 µm

[Ref.: #31482]	Cell shape	rod-shaped

[Ref.: #31482]	Motility	yes

[Ref.: #31482]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6362]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #6362]

Culture medium growth

[Ref.: #6362]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6362]

Culture medium composition

expand / minimize

[Ref.: #6362]

Culture medium

NITRINCOLA MEDIUM (DSMZ Medium 1174)

[Ref.: #6362]

Culture medium growth

[Ref.: #6362]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6362]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #6362]	growth	28 °C
[Ref.: #6362]	growth	37 °C
[Ref.: #31482]	optimum	37 °C

[Ref.: #6362]	Temperature range	mesophilic
[Ref.: #31482]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31482]			optimum	9
[Ref.: #31482]			growth	7.5-11.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31482]

Oxygen tolerance

aerobe

[Ref.: #31482]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31482]		NaCl		growth	1.16-7.54	%
[Ref.: #31482]		NaCl		optimum	4.64	%

[Ref.: #31482]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31482]	acetate ChEBI	+	carbon source
[Ref.: #31482]	lactate ChEBI	+	carbon source
[Ref.: #31482]	malate ChEBI	+	carbon source
[Ref.: #31482]	pyruvate ChEBI	+	carbon source
[Ref.: #31482]	succinate ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #31482]		catalase	+	1.11.1.6
[Ref.: #31482]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	lysine metabolism	71.43	30 of 42
[Ref.: #66794]	purine metabolism	71.28	67 of 94
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	phenol degradation	65	13 of 20
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	oxidative phosphorylation	63.74	58 of 91
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	sulfate reduction	61.54	8 of 13
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	polyamine pathway	60.87	14 of 23
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	pentose phosphate pathway	45.45	5 of 11
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	elloramycin biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin B1 metabolism	38.46	5 of 13
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
		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.: #6362]	Sample type/isolated from	decomposing wood taken from the shore of Soap Lake, a meromictic, saline, alkaline lake
[Ref.: #6362]	Geographic location (country and/or sea, region)	Washington State, Grant County
[Ref.: #6362]	Country	USA
[Ref.: #6362]	Country ISO 3 Code	USA
[Ref.: #6362]	Continent	North America
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Decomposing plant
#Host Body Product	#Plant	#Timber
#Condition	#Alkaline	-
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY567473 (>99% sequence identity) for Nitrincola lacisaponensis subclade from Microbeatlas

Aquatic Samples	138
Soil Samples	18
Animal Samples	185
Plant Samples	17
Total Samples	358

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

[Ref.: #6362]

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.: #6362]	Nitrincola lacisaponensis strain 4CA 16S ribosomal RNA gene, partial sequence	AY567473	1432	ENA	267850 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Nitrincola lacisaponensis 4CA	GCA_000691225	contig	GenBank	267850 tax ID	*
[Ref.: #66792]	Nitrincola lacisaponensis 4CA	2576861796	draft	JGI IMG/M	267850 tax ID	*

[Ref.: #6362]	GC-content	47.4 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #31482]	GC-content	47.4 mol%

Availability in culture collections External links

[Ref.: #6362]

Culture collection no.

DSM 16316, ATCC BAA-920

[Ref.: #80517]

SI-ID 405043

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nitrincola alkalisediminis sp. nov., an alkaliphilic bacterium isolated from an alkaline lake.	Joshi A, Thite S, Kulkarni G, Dhotre D, Joseph N, Venkata Ramana V, Polkade A, Shouche Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.000868	2015	*
Phylogeny	Nitrincola nitratireducens sp. nov. isolated from a haloalkaline crater lake.	Singh A, Vaidya B, Tanuku NR, Pinnaka AK	Syst Appl Microbiol	10.1016/j.syapm.2015.09.002	2015	*
Phylogeny	Nitrincola lacisaponensis gen. nov., sp. nov., a novel alkaliphilic bacterium isolated from an alkaline, saline lake.	Dimitriu PA, Shukla SK, Conradt J, Marquez MC, Ventosa A, Maglia A, Peyton BM, Pinkart HC, Mormile MR	Int J Syst Evol Microbiol	10.1099/ijs.0.63647-0	2005	*

References

#6362

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16316

#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 )

#31482

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 #27780 (see below)

#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 .

#80517

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-ID405043.1 )

#27780

IJSEM 2273 2005 ( DOI 10.1099/ijs.0.63647-0 , PubMed 16280482 )

* These data were automatically processed and therefore are not curated

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