Gemmobacter aquatilis (DSM 3857, ATCC 49971, IFAM 1031)

Name: Gemmobacter aquatilis (DSM 3857, ATCC 49971, IFAM 1031)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13663

Type strain

Culture col. no. DSM 3857 ATCC 49971 IFAM 1031

NCBI tax ID(s) 933059

Special Collections DSMZ

History <- E. Stackebrandt <- P. Hirsch

Links

Gemmobacter aquatilis DSM 3857 is a bacterium that was isolated from forest pond.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 42783

ATCC 49971,DSM 3857

@ref 20215

Last LPSN update 2026-02-09 11:21:12

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Gemmobacter

Species Gemmobacter aquatilis

Full scientific name Gemmobacter aquatilis Rothe et al. 1988

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	99.5
125439	negative	95.6

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1485	PYGV AGAR (DSMZ Medium 621)		Medium recipe at MediaDive	Name: PYGV AGAR (DSMZ Medium 621) Composition: Agar 15.0 g/l MgSO4 x 7 H2O 0.625264 g/l Glucose 0.25 g/l Peptone 0.25 g/l Yeast extract 0.25 g/l Nitrilotriacetic acid 0.210526 g/l CaCl2 x 2 H2O 0.0703158 g/l FeSO4 x 7 H2O 0.00208422 g/l Na2MoO4 x 2 H2O 0.000266736 g/l Pyridoxine hydrochloride 0.0001 g/l p-Aminobenzoic acid 5e-05 g/l D-Calcium pantothenate 5e-05 g/l Nicotinamide 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavine 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Metall salt sol. 44 Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
1485	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	96.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	ppGpp biosynthesis	100	4 of 4
66794	CMP-KDO biosynthesis	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	Entner Doudoroff pathway	100	10 of 10
66794	octane oxidation	100	3 of 3
66794	ethanol fermentation	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	allantoin degradation	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	purine metabolism	86.17	81 of 94
66794	propanol degradation	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	glutathione metabolism	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	vitamin B1 metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	pyrimidine metabolism	82.22	37 of 45
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	proline metabolism	81.82	9 of 11
66794	degradation of sugar alcohols	81.25	13 of 16
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	myo-inositol biosynthesis	80	8 of 10
66794	creatinine degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	photosynthesis	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	lysine metabolism	78.57	33 of 42
66794	d-mannose degradation	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	histidine metabolism	75.86	22 of 29
66794	ketogluconate metabolism	75	6 of 8
66794	cyclohexanol degradation	75	3 of 4
66794	arginine metabolism	75	18 of 24
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	tyrosine metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	urea cycle	69.23	9 of 13
66794	oxidative phosphorylation	69.23	63 of 91
66794	tryptophan metabolism	68.42	26 of 38
66794	methane metabolism	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	pentose phosphate pathway	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	methionine metabolism	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	vitamin K metabolism	60	3 of 5
66794	3-chlorocatechol degradation	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	biotin biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	degradation of hexoses	50	9 of 18
66794	quinate degradation	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	sulfate reduction	46.15	6 of 13
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	factor 420 biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	starch degradation	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	carnitine metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	d-xylose degradation	36.36	4 of 11
66794	degradation of sugar acids	36	9 of 25
66794	IAA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	arachidonic acid metabolism	33.33	6 of 18
66794	chlorophyll metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Terrestrial	#Forest

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
1485	forest pond	Michigan, Augusta	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence FR733676 (>99% sequence identity) for Gemmobacter aquatilis from Microbeatlas

Aquatic Samples	92
Soil Samples	9
Animal Samples	40
Plant Samples	4
Total Samples	145

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1485	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	IMG-taxon 2615840721 annotated assembly for Gemmobacter aquatilis DSM 3857	scaffold	GCA_900110025	933059.3	2615840721	933059	70.93

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
1485	Gemmobacter aquatilis partial 16S rRNA gene, type strain DSM3857T	FR733676	1454		933059

GC content

1485

GC-content (mol%)63.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Gemmobacter aquatilis DSM 3857
NCBI: GCA_900110025

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	54.10	no
125439	motility	BacteriaNetⓘ	yes	50.50	no
125439	gram_stain	BacteriaNetⓘ	negative	95.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	96.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gemmobacter aquatilis DSM 3857
NCBI: GCA_900110025.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.50	no
125438	anaerobic	anaerobicⓘ	no	92.95	no
125438	aerobic	aerobicⓘ	yes	80.53	no
125438	spore-forming	spore-formingⓘ	no	87.90	no
125438	thermophilic	thermophileⓘ	no	97.75	yes
125438	flagellated	motile2+ⓘ	no	65.20	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine.	Zeng XC, E G, Wang J, Wang N, Chen X, Mu Y, Li H, Yang Y, Liu Y, Wang Y.	Appl Environ Microbiol	10.1128/aem.02190-16	2016
	Genomic Insights into Denitrifying Methane-Oxidizing Bacteria Gemmobacter fulva sp. Nov., Isolated from an Anabaena Culture.	Jin L, Jin CZ, Lee HG, Lee CS.	Microorganisms	10.3390/microorganisms9122423	2021
Enzymology	Structural and kinetic characterization of (S)-1-amino-2-propanol kinase from the aminoacetone utilization microcompartment of Mycobacterium smegmatis.	Mallette E, Kimber MS.	J Biol Chem	10.1074/jbc.ra118.005485	2018
Genetics	Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria.	Hordt A, Lopez MG, Meier-Kolthoff JP, Schleuning M, Weinhold LM, Tindall BJ, Gronow S, Kyrpides NC, Woyke T, Goker M.	Front Microbiol	10.3389/fmicb.2020.00468	2020
Phylogeny	Gemmobacter denitrificans sp. nov., a denitrifying bacterium, isolated from pond water for Litopenaeus vannamei.	Zhang M, Zhang Y, Yang F, Yao Q, Zhu H.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006430	2024
Phylogeny	Gemmobacter serpentinus sp. nov., isolated from conserved forages.	Lim K, Kannan AD, Shobnam N, Mahmood M, Lee J, Im J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004276	2020
Phylogeny	Gemmobacter tilapiae sp. nov., a poly-beta-hydroxybutyrate-accumulating bacterium isolated from a freshwater pond.	Sheu SY, Sheu DS, Sheu FS, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.044735-0	2012
Phylogeny	Description of Gemmobacter fontiphilus sp. nov., isolated from a freshwater spring, reclassification of Catellibacterium nectariphilum as Gemmobacter nectariphilus comb. nov., Catellibacterium changlense as Gemmobacter changlensis comb. nov., Catellibacterium aquatile as Gemmobacter aquaticus nom. nov., Catellibacterium caeni as Gemmobacter caeni comb. nov., Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and of Gemmobacter aquatilis.	Chen WM, Cho NT, Huang WC, Young CC, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijs.0.042051-0	2012

References

#1485	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3857
#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 )
#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 .
#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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Gemmobacter aquatilis (DSM 3857, ATCC 49971, IFAM 1031)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900110025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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