Aquabacter spiritensis (DSM 9035, ATCC 43981, LMG 8611)

Name: Aquabacter spiritensis (DSM 9035, ATCC 43981, LMG 8611)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6157

Type strain

Strain Designation SPL-1

Culture col. no. DSM 9035 ATCC 43981 LMG 8611 SPL-1 CCUG 58315

NCBI tax ID(s) 933073

Special Collections DSMZ CCUG

Links

Aquabacter spiritensis SPL-1 is a mesophilic prokaryote that was isolated from water .

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 9843

LMG 8611,ATCC 43981,DSM 9035,CCUG 58315

@ref 20215

Last LPSN update 2025-12-16 09:48:15

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Xanthobacteraceae

Genus Aquabacter

Species Aquabacter spiritensis

Full scientific name Aquabacter spiritensis Irgens et al. 1993

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	97
125438	negative	98.4

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3393	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
3393	MMB MEDIUM (DSMZ Medium 628)		Medium recipe at MediaDive	Name: MMB MEDIUM (DSMZ Medium 628) Composition: Glucose 1.0 g/l MgSO4 x 7 H2O 0.594 g/l (NH4)2SO4 0.25 g/l Nitrilotriacetic acid 0.2 g/l Yeast extract 0.15 g/l Peptone 0.15 g/l CaCl2 x 2 H2O 0.0667 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l (NH4)6Mo7O24 x 4 H2O 0.000185 g/l MnSO4 x H2O 0.000154 g/l Calcium pantothenate 5e-05 g/l Pyridoxine hydrochloride 5e-05 g/l Riboflavin 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Biotin 2e-05 g/l Folic acid 2e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Vitamin B12 1e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
3393	positive	growth	28	mesophilic
3393	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	94.9

Spore formation

@ref	Spore formation	Confidence
125439		95.7

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	3-chlorocatechol degradation	100	5 of 5
66794	Entner Doudoroff pathway	100	10 of 10
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	methanofuran biosynthesis	100	5 of 5
66794	ethanol fermentation	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	resorcinol degradation	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	L-lactaldehyde degradation	100	3 of 3
66794	acetoin degradation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	gallate degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	cyanate degradation	100	3 of 3
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	citric acid cycle	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	vitamin B12 metabolism	91.18	31 of 34
66794	4-hydroxyphenylacetate degradation	90	9 of 10
66794	starch degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	lipid A biosynthesis	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	phenol degradation	85	17 of 20
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	proline metabolism	81.82	9 of 11
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	degradation of sugar acids	80	20 of 25
66794	factor 420 biosynthesis	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	tryptophan metabolism	78.95	30 of 38
66794	heme metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	non-pathway related	76.32	29 of 38
66794	alanine metabolism	75.86	22 of 29
66794	isoleucine metabolism	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	3-phenylpropionate degradation	73.33	11 of 15
66794	methionine metabolism	73.08	19 of 26
66794	pentose phosphate pathway	72.73	8 of 11
66794	vitamin B6 metabolism	72.73	8 of 11
66794	glutathione metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	glycolysis	70.59	12 of 17
66794	purine metabolism	70.21	66 of 94
66794	coenzyme M biosynthesis	70	7 of 10
66794	oxidative phosphorylation	67.03	61 of 91
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	IAA biosynthesis	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	lipid metabolism	64.52	20 of 31
66794	metabolism of disaccharids	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	sulfate reduction	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	methanogenesis from CO2	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	lysine metabolism	57.14	24 of 42
66794	tyrosine metabolism	57.14	8 of 14
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	carotenoid biosynthesis	54.55	12 of 22
66794	arginine metabolism	54.17	13 of 24
66794	degradation of pentoses	53.57	15 of 28
66794	polyamine pathway	52.17	12 of 23
66794	glycogen biosynthesis	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	myo-inositol biosynthesis	50	5 of 10
66794	degradation of sugar alcohols	50	8 of 16
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	nitrate assimilation	44.44	4 of 9
66794	ascorbate metabolism	40.91	9 of 22
66794	glycine betaine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	degradation of hexoses	38.89	7 of 18
66794	arachidonic acid metabolism	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	cholesterol biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Aquatic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3393	water (5 m depth)	Spirit Lake, Washinghton	USA	USA	North America
61658	Water,5.0 m depth	Washington,Spirit Lake	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3393	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM434618v1 assembly for Aquabacter spiritensis DSM 9035	scaffold	GCA_004346185	933073.3	2784746799	933073	66.72

Genome browser: GCA_004346185

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
3393	Aquabacter spiritensis partial 16S rRNA gene, type strain DSM9035T	FR733686	1474		933073

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Aquabacter spiritensis DSM 9035
NCBI: GCA_004346185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.70	no
125439	motility	BacteriaNetⓘ	yes	52.80	no
125439	gram_stain	BacteriaNetⓘ	negative	97.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Aquabacter spiritensis DSM 9035
NCBI: GCA_004346185.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.40	no
125438	anaerobic	anaerobicⓘ	no	89.82	no
125438	aerobic	aerobicⓘ	yes	82.30	no
125438	spore-forming	spore-formingⓘ	no	83.60	no
125438	thermophilic	thermophileⓘ	no	97.53	yes
125438	flagellated	motile2+ⓘ	yes	68.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains.	Volpiano CG, Sant'Anna FH, Ambrosini A, de Sao Jose JFB, Beneduzi A, Whitman WB, de Souza EM, Lisboa BB, Vargas LK, Passaglia LMP.	Front Microbiol	10.3389/fmicb.2021.614957	2021
Phylogeny	Characterization of a novel root-associated diazotrophic rare PGPR taxa, Aquabacter pokkalii sp. nov., isolated from pokkali rice: new insights into the plant-associated lifestyle and brackish adaptation.	Sunithakumari VS, Menon RR, Suresh GG, Krishnan R, Rameshkumar N.	BMC Genomics	10.1186/s12864-024-10332-z	2024
Phylogeny	Aquabacter cavernae sp. nov., a bacterium isolated from cave soil.	Duo JL, Cha QY, Zhou XK, Zhang TK, Qin SC, Yang PX, Zhu ML, Mo MH, Duan YQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003585	2019

References

#3393	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 9035
#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 )
#61658	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 58315
#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 )
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Aquabacter spiritensis (DSM 9035, ATCC 43981, LMG 8611)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004346185

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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