Noviherbaspirillum denitrificans (JCM 17722, ATCC TSD-69, TSA 40)

Cell morphology

Colony morphology

Multimedia

• @ref:	68999
  multimedia content:	DSM_113107.jpg
  multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_113107.jpg
  caption:	Micrograph of DSM 113107. Scale bar represents 2 um.
  intellectual property rights:	Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
68999	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
43245	Reasoner's 2A agar (R2A)
43245	DNBNS medium			100-fold diluted nutrient broth (DNB; Difco) supplemented with 3 mM nitrate and 4.4 mM succinate
43245	nutritient agar
43245	trypticase soy broth (TSB)

Culture temp

Culture pH

Oxygen tolerance

Halophily

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43245	52682 ChEBI	1,2-butandiol	-	growth
43245	30089 ChEBI	acetate	+	electron donor
43245	17968 ChEBI	butyrate	+	electron donor
43245	62968 ChEBI	cellulose	-	growth
43245	17045 ChEBI	dinitrogen oxide	+	electron acceptor
43245	16236 ChEBI	ethanol	-	growth
43245	28757 ChEBI	fructose	-	growth
43245	28260 ChEBI	galactose	-	growth
43245	24265 ChEBI	gluconate	-	growth
43245	17234 ChEBI	glucose	-	growth
43245	17754 ChEBI	glycerol	+	electron donor
43245	24996 ChEBI	lactate	+	electron donor
43245	17716 ChEBI	lactose	-	growth
43245	17306 ChEBI	maltose	-	growth
43245	37684 ChEBI	mannose	-	growth
43245	17632 ChEBI	nitrate	+	electron donor
43245	16301 ChEBI	nitrite	+	electron acceptor
43245	15361 ChEBI	pyruvate	+	electron donor
43245	30911 ChEBI	sorbitol	-	growth
43245	28017 ChEBI	starch	-	growth
43245	30031 ChEBI	succinate	+	electron donor
43245	53423 ChEBI	tween 40	+	growth
43245	53426 ChEBI	tween 80	+	growth
43245	31011 ChEBI	valerate	+	electron donor
43245	18222 ChEBI	xylose	-	growth

Enzymes

@ref	Value	Activity	Ec
43245	catalase	+	1.11.1.6
43245	cytochrome oxidase	+	1.9.3.1
43245	urease	-	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	butanoate fermentation	100	4 of 4
66794	Entner Doudoroff pathway	100	10 of 10
66794	adipate degradation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	citric acid cycle	100	14 of 14
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	propanol degradation	100	7 of 7
66794	aspartate and asparagine metabolism	100	9 of 9
66794	L-lactaldehyde degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	valine metabolism	100	9 of 9
66794	resorcinol degradation	100	2 of 2
66794	hydrogen production	100	5 of 5
66794	cyanate degradation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	ubiquinone biosynthesis	100	7 of 7
66794	denitrification	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	suberin monomers biosynthesis	100	2 of 2
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	starch degradation	90	9 of 10
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	gluconeogenesis	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	phenol degradation	85	17 of 20
66794	vitamin B1 metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	purine metabolism	82.98	78 of 94
66794	glycolysis	82.35	14 of 17
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	vitamin B6 metabolism	81.82	9 of 11
66794	proline metabolism	81.82	9 of 11
66794	lysine metabolism	80.95	34 of 42
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	3-chlorocatechol degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	alanine metabolism	79.31	23 of 29
66794	tryptophan metabolism	78.95	30 of 38
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	cysteine metabolism	77.78	14 of 18
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	ketogluconate metabolism	75	6 of 8
66794	androgen and estrogen metabolism	75	12 of 16
66794	flavin biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	glutathione metabolism	71.43	10 of 14
66794	lipid metabolism	70.97	22 of 31
66794	methionine metabolism	69.23	18 of 26
66794	urea cycle	69.23	9 of 13
66794	pyrimidine metabolism	68.89	31 of 45
66794	degradation of sugar alcohols	68.75	11 of 16
66794	non-pathway related	68.42	26 of 38
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	nitrate assimilation	66.67	6 of 9
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	oxidative phosphorylation	65.93	60 of 91
66794	metabolism of disaccharids	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	sulfate reduction	61.54	8 of 13
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	glycogen metabolism	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	vitamin K metabolism	60	3 of 5
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	catecholamine biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	selenocysteine biosynthesis	50	3 of 6
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	degradation of sugar acids	44	11 of 25
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	vitamin B12 metabolism	41.18	14 of 34
66794	arachidonate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	cholesterol biosynthesis	36.36	4 of 11
66794	ascorbate metabolism	36.36	8 of 22
66794	degradation of pentoses	35.71	10 of 28
66794	polyamine pathway	34.78	8 of 23
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	coenzyme M biosynthesis	30	3 of 10
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	carotenoid biosynthesis	27.27	6 of 22
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	methanogenesis from CO2	25	3 of 12

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence AB542397 (>99% sequence identity) for Noviherbaspirillum denitrificans from Microbeatlas

Aquatic Samples	168
Soil Samples	2079
Animal Samples	245
Plant Samples	396
Total Samples	2888

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID
67770	ASM221144v1 assembly for Noviherbaspirillum denitrificans TSA40	scaffold	GCA_002211445	1968433.3	2802429631	1968433

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
43245	Herbaspirillum sp. TSA40 gene for 16S ribosomal RNA, partial sequence, strain: TSA40	AB542397	1458		1968433

GC content

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	A small step to discover candidate biological control agents from preexisting bioresources by using novel nonribosomal peptide synthetases hidden in activated sludge metagenomes.	Tomita S, Kuroda K, Narihiro T.	PLoS One	10.1371/journal.pone.0294843	2023
Phylogeny	Massilia horti sp. nov. and Noviherbaspirillum arenae sp. nov., two novel soil bacteria of the Oxalobacteraceae.	Peta V, Raths R, Bucking H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004765	2021
Phylogeny	Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.	Ishii S, Ashida N, Ohno H, Segawa T, Yabe S, Otsuka S, Yokota A, Senoo K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001875	2017