Niabella soli (DSM 19437, KACC 12604, JS13-8)

Cell morphology

Pigmentation

Multimedia

• @ref:	66793
  multimedia content:	EM_DSM_19437_1.jpg
  multimedia.multimedia content:	EM_DSM_19437_1.jpg
  caption:	electron microscopic image
  intellectual property rights:	© HZI/Manfred Rohde
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
8016	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

Culture pH

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32318	22599 ChEBI	arabinose	+	carbon source
32318	4853 ChEBI	esculin	+	hydrolysis
32318	17234 ChEBI	glucose	+	carbon source
32318	17306 ChEBI	maltose	+	carbon source
32318	37684 ChEBI	mannose	+	carbon source
32318	28053 ChEBI	melibiose	+	carbon source
32318	506227 ChEBI	N-acetylglucosamine	+	carbon source
32318	26546 ChEBI	rhamnose	+	carbon source
32318	17814 ChEBI	salicin	+	carbon source
32318	17992 ChEBI	sucrose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32318	acid phosphatase	+	3.1.3.2
32318	alkaline phosphatase	+	3.1.3.1
32318	alpha-galactosidase	+	3.2.1.22

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	adipate degradation	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	coenzyme A metabolism	100	4 of 4
66794	kanosamine biosynthesis II	100	2 of 2
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	starch degradation	100	10 of 10
66794	sulfopterin metabolism	100	4 of 4
66794	denitrification	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	lactate fermentation	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	photosynthesis	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	valine metabolism	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	purine metabolism	76.6	72 of 94
66794	ppGpp biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	degradation of pentoses	75	21 of 28
66794	lipid metabolism	74.19	23 of 31
66794	pyrimidine metabolism	73.33	33 of 45
66794	methionine metabolism	73.08	19 of 26
66794	d-xylose degradation	72.73	8 of 11
66794	pentose phosphate pathway	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	d-mannose degradation	66.67	6 of 9
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	formaldehyde oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	glycolysis	64.71	11 of 17
66794	citric acid cycle	64.29	9 of 14
66794	lysine metabolism	64.29	27 of 42
66794	vitamin B6 metabolism	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	histidine metabolism	62.07	18 of 29
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of sugar acids	60	15 of 25
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	alanine metabolism	58.62	17 of 29
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	non-pathway related	57.89	22 of 38
66794	tyrosine metabolism	57.14	8 of 14
66794	glutathione metabolism	57.14	8 of 14
66794	degradation of hexoses	55.56	10 of 18
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	proline metabolism	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	vitamin B1 metabolism	53.85	7 of 13
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	sulfate reduction	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	daunorubicin biosynthesis	44.44	4 of 9
66794	ascorbate metabolism	40.91	9 of 22
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	vitamin K metabolism	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	metabolism of disaccharids	36.36	4 of 11
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	oxidative phosphorylation	32.97	30 of 91
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	polyamine pathway	30.43	7 of 23
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	phenol degradation	25	5 of 20
66794	toluene degradation	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence EF592608 (>99% sequence identity) for Niabella soli subclade from Microbeatlas

Aquatic Samples	630
Soil Samples	564
Animal Samples	203
Plant Samples	284
Total Samples	1681

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM24311v3 assembly for Niabella soli DSM 19437 JS13-8; DSM 19437	complete	GCA_000243115	929713.18	2506783006	929713	98.94
66792	Niabella soli DSM 19437	contig		929713.3		929713	73.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8016	Niabella soli strain JS13-8 16S ribosomal RNA gene, partial sequence	EF592608	1390		929713

GC content

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	A Multicolor Fluorescence in situ Hybridization Approach Using an Extended Set of Fluorophores to Visualize Microorganisms.	Lukumbuzya M, Schmid M, Pjevac P, Daims H.	Front Microbiol	10.3389/fmicb.2019.01383	2019
	Classifying nitrilases as aliphatic and aromatic using machine learning technique.	Sharma N, Verma R, Savitri, Bhalla TC.	3 Biotech	10.1007/s13205-018-1102-9	2018
Genetics	Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)).	Anderson I, Munk C, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Mavromatis K, Pagani I, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Rohde M, Tindall BJ, Goker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Ivanova N	Stand Genomic Sci	10.4056/sigs.3117229	2012
Phylogeny	Niabella hibiscisoli sp. nov., isolated from soil of a Rose of Sharon garden.	Ngo HTT, Trinh H, Yan ZF, Moya G, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001595	2017
Phylogeny	Niabella ginsenosidivorans sp. nov., isolated from compost.	Yi KJ, Im WT, Kim DW, Liu QM, Kim SK	J Microbiol	10.1007/s12275-015-5463-z	2015
Phylogeny	Niabella yanshanensis sp. nov., isolated from the soybean rhizosphere.	Wang H, Zhang YZ, Man CX, Chen WF, Sui XH, Li Y, Zhang XX, Chen WX	Int J Syst Evol Microbiol	10.1099/ijs.0.010447-0	2009
Phylogeny	Niabella ginsengisoli sp. nov., isolated from soil cultivated with Korean ginseng.	Weon HY, Yoo SH, Kim BY, Son JA, Kim YJ, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.004333-0	2009
Phylogeny	Niabella soli sp. nov., isolated from soil from Jeju Island, Korea.	Weon HY, Kim BY, Joa JH, Kwon SW, Kim WG, Koo BS	Int J Syst Evol Microbiol	10.1099/ijs.0.65304-0	2008