Archive BacDiveID:10.13145/bacdive352.20230509.8.1

Strain identifier

BacDive ID: 352

Type strain:

Species: Derxia gummosa

Strain Designation: II

Strain history: IAM 13946 <-- DSM 723 <-- J. De Ley <-- NCIB 9064 <-- H. L. Jensen strain II <-- R. Bhattacharya.

NCBI tax ID(s): 1121388 (strain), 203699 (species)

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

General

@ref: 369

BacDive-ID: 352

DSM-Number: 723

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Derxia gummosa II is a mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax id	Matching level
203699	species
1121388	strain

strain history

@ref	history
369	<- J. De Ley <- NCIB <- H.L. Jensen, II <- R. Bhattacharya
67770	IAM 13946 <-- DSM 723 <-- J. De Ley <-- NCIB 9064 <-- H. L. Jensen strain II <-- R. Bhattacharya.

doi: 10.13145/bacdive352.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Betaproteobacteria
order: Burkholderiales
family: Alcaligenaceae
genus: Derxia
species: Derxia gummosa
full scientific name: Derxia gummosa Jensen et al. 1960 (Approved Lists 1980)

@ref: 369

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Alcaligenaceae

genus: Derxia

species: Derxia gummosa

full scientific name: Derxia gummosa Jensen et al. 1960

strain designation: II

type strain: yes

Morphology

multimedia

@ref	multimedia content	caption	intellectual property rights
66793	EM_DSM_723_1.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_723_2.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_723_3.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_723_4.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_723_5.jpg	electron microscopic image	© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
369	HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428)	yes	https://mediadive.dsmz.de/medium/428	Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water
369	MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81)	yes	https://mediadive.dsmz.de/medium/81	Name: MINERAL MEDIUM FOR CHEMOLITHOTROPHIC GROWTH (H-3) (DSMZ Medium 81) Composition: Agar 20.1005 g/l Na2HPO4 x 2 H2O 2.91457 g/l KH2PO4 2.31156 g/l NH4Cl 1.00503 g/l MgSO4 x 7 H2O 0.502512 g/l Ferric ammonium citrate 0.0502513 g/l CaCl2 x 2 H2O 0.0100503 g/l NaVO3 x H2O 0.00502512 g/l Calcium pantothenate 0.00251256 g/l Pyridoxine hydrochloride 0.00251256 g/l Nicotinic acid 0.00251256 g/l Thiamine-HCl x 2 H2O 0.00251256 g/l H3BO3 0.00150754 g/l CoCl2 x 6 H2O 0.00100503 g/l Riboflavin 0.000502513 g/l ZnSO4 x 7 H2O 0.000502513 g/l MnCl2 x 4 H2O 0.000150754 g/l Na2MoO4 x 2 H2O 0.000150754 g/l NiCl2 x 6 H2O 0.000100503 g/l CuCl2 x 2 H2O 5.02513e-05 g/l Vitamin B12 5.02513e-05 g/l Folic acid 1.00503e-05 g/l Biotin 5.02513e-06 g/l Distilled water
369	NUTRIENT AGAR (DSMZ Medium 1)	yes	https://mediadive.dsmz.de/medium/1	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
369	positive	growth	28	mesophilic
67770	positive	growth	25	mesophilic

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
369	soil	West Bengal	India	IND	Asia
59092	Soil
67770	Soil	West Bengal	India	IND	Asia

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

taxonmaps

@ref: 69479
File name: preview.99_53996.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_173;96_576;97_673;98_782;99_53996&stattab=map
Last taxonomy: Derxia gummosa
16S sequence: AB681840
Sequence Identity:
Total samples: 265
soil counts: 18
aquatic counts: 188
animal counts: 37
plant counts: 22

Safety information

risk assessment

@ref: 369
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Derxia gummosa gene for 16S ribosomal RNA, complete sequence, strain:IAM13946	AB089482	1449	ena	203699
20218	Derxia gummosa gene for 16S rRNA, partial sequence, strain: NBRC 102506	AB681840	1456	ena	203699

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Derxia gummosa DSM 723	1121388.4	wgs	patric	1121388
66792	Derxia lacustris strain HL-12	764842.44	wgs	patric	764842
66792	Derxia gummosa DSM 723	2529292503	draft	img	1121388
67770	Derxia gummosa DSM 723	GCA_000482785	scaffold	ncbi	1121388

GC content

@ref: 369
GC-content: 69.2

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	yes	86.225	no
flagellated	yes	69.958	no
gram-positive	no	98.993	no
anaerobic	no	97.592	no
aerobic	yes	88.461	no
halophile	no	96.593	no
spore-forming	no	94.692	no
glucose-util	yes	83.026	no
thermophile	no	98.076	yes
glucose-ferment	no	90.616	no

External links

@ref: 369

culture collection no.: DSM 723, ATCC 15994, NCIB 9064, CCUG 51006, LMG 3977, NRRL B-4319, NRRL B-14655, JCM 20996, BCRC 80374, CECT 841, IAM 13946, NBRC 102506, NCIMB 9064

straininfo link

@ref: 70032
straininfo: 2182

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	22659506	Derxia lacustris sp. nov., a nitrogen-fixing bacterium isolated from a freshwater lake.	Chen WM, Huang WC, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijs.0.041186-0	2012	Alcaligenaceae/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Lakes/microbiology, Molecular Sequence Data, Nitrogen Fixation, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Water Microbiology	Genetics
Phylogeny	28950929	Quisquiliibacterium transsilvanicum gen. nov., sp. nov., a novel betaproteobacterium isolated from a waste-treating bioreactor.	Felfoldi T, Fiko RD, Mentes A, Kovacs E, Mathe I, Schumann P, Toth E	Int J Syst Evol Microbiol	10.1099/ijsem.0.002368	2017	Alcaligenaceae/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Bioreactors/microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Romania, Sequence Analysis, DNA, Sewage/microbiology, Ubiquinone/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
369	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 723)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-723
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
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
59092	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 51006)	https://www.ccug.se/strain?id=51006
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)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life	35: 676-683 2017	28604660
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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
70032	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID2182.1	StrainInfo: A central database for resolving microbial strain identifiers