Archive BacDiveID:10.13145/bacdive13663.20230509.8.1

Strain identifier

BacDive ID: 13663

Type strain:

Species: Gemmobacter aquatilis

Strain history: <- E. Stackebrandt <- P. Hirsch

NCBI tax ID(s): 933059 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 1485

BacDive-ID: 13663

DSM-Number: 3857

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Gemmobacter aquatilis DSM 3857 is a mesophilic, Gram-negative bacterium that was isolated from forest pond.

NCBI tax id

NCBI tax id: 933059
Matching level: species

strain history

@ref: 1485
history: <- E. Stackebrandt <- P. Hirsch

doi: 10.13145/bacdive13663.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Rhodobacterales
family: Paracoccaceae
genus: Gemmobacter
species: Gemmobacter aquatilis
full scientific name: Gemmobacter aquatilis Rothe et al. 1988

@ref: 1485

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Gemmobacter

species: Gemmobacter aquatilis

full scientific name: Gemmobacter aquatilis Rothe et al. 1988 emend. Chen et al. 2013

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.999

Culture and growth conditions

culture medium

@ref: 1485
name: PYGV AGAR (DSMZ Medium 621)
growth: yes
link: https://mediadive.dsmz.de/medium/621
composition: 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: 1485
growth: positive
type: growth
temperature: 30
range: mesophilic

Physiology and metabolism

spore formation

@ref: 69480
spore formation: no
confidence: 99.999

Isolation, sampling and environmental information

isolation

@ref: 1485
sample type: forest pond
geographic location: Michigan, Augusta
country: USA
origin.country: USA
continent: North America

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_98975.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_926;97_3623;98_15523;99_98975&stattab=map
Last taxonomy: Gemmobacter aquatilis
16S sequence: FR733676
Sequence Identity:
Total samples: 145
soil counts: 9
aquatic counts: 92
animal counts: 40
plant counts: 4

Safety information

risk assessment

@ref: 1485
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 1485
description: Gemmobacter aquatilis partial 16S rRNA gene, type strain DSM3857T
accession: FR733676
length: 1454
database: ena
NCBI tax ID: 933059

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Gemmobacter aquatilis DSM 3857	GCA_900110025	scaffold	ncbi	933059
66792	Gemmobacter aquatilis strain DSM 3857	933059.3	wgs	patric	933059
66792	Gemmobacter aquatilis DSM 3857	2615840721	draft	img	933059

GC content

@ref: 1485
GC-content: 63.0

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	79	no
glucose-ferment	no	86.285	no
motile	no	75.407	no
flagellated	no	93.009	no
gram-positive	no	98.789	no
anaerobic	no	97.331	no
aerobic	yes	79.728	no
halophile	no	87.997	no
spore-forming	no	96.873	no
thermophile	no	96.803	yes
glucose-util	yes	88.613	no

External links

@ref: 1485

culture collection no.: DSM 3857, ATCC 49971, IFAM 1031

straininfo link

@ref: 82846
straininfo: 42783

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	22493172	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	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water/microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Natural Springs/microbiology, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/isolation & purification, Sequence Analysis, DNA, Taiwan	Genetics
Phylogeny	22888190	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	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water/microbiology, Hydroxybutyrates/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Polyesters/metabolism, Ponds, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification/metabolism, Sequence Analysis, DNA, Taiwan	Metabolism
Phylogeny	32553048	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	Animal Feed/microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Kansas, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
1485	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3857)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-3857
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
82846	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID42783.1	StrainInfo: A central database for resolving microbial strain identifiers