Archive BacDiveID:10.13145/bacdive6081.20240916.9.1

Strain identifier

BacDive ID: 6081

Type strain:

Species: Salinicola socius

Strain Designation: SMB35

Strain history: Emendations: de la Haba et al. 2010 de la Haba RR, Sanchez-Porro C, Marquez MC, Ventosa A. Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and S

NCBI tax ID(s): 404433 (species)

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

General

@ref: 8398

BacDive-ID: 6081

DSM-Number: 19940

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

description: Salinicola socius SMB35 is a motile bacterium that was isolated from soil of salt mines.

NCBI tax id

NCBI tax id: 404433
Matching level: species

strain history

@ref	history
8398	<- E. G. Plotnikova, IEGM; SMB35 <- L. N. Anan'ina and E. G. Plotnikova
67772	Emendations: de la Haba et al. 2010 de la Haba RR, Sanchez-Porro C, Marquez MC, Ventosa A. Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and S

doi: 10.13145/bacdive6081.20240916.9.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Oceanospirillales
family: Halomonadaceae
genus: Salinicola
species: Salinicola socius
full scientific name: Salinicola socius Anan'ina et al. 2008

@ref: 8398

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Salinicola

species: Salinicola socius

full scientific name: Salinicola socius Anan'ina et al. 2008 emend. de la Haba et al. 2010

strain designation: SMB35

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.969

Culture and growth conditions

culture medium

@ref: 8398
name: SMB MEDIUM (DSMZ Medium 1185)
growth: yes
link: https://mediadive.dsmz.de/medium/1185
composition: Name: SMB MEDIUM (DSMZ Medium 1185) Composition: NaCl 50.0 g/l Agar 15.0 g/l Tryptone 5.0 g/l Na2HPO4 3.0 g/l KH2PO4 2.0 g/l Yeast extract 2.0 g/l NH4NO3 1.0 g/l MgSO4 x 7 H2O 0.2 g/l Na2CO3 0.1 g/l MnSO4 x 2 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water

culture temp

@ref	growth	type	temperature
8398	positive	growth	28
67772	positive	optimum	30-37
67772	positive	minimum	4
67772	positive	maximum	45

culture pH

@ref	ability	type	pH
67772	positive	maximum	8.0
67772	positive	minimum	6.0

Physiology and metabolism

spore formation

@ref: 69481
spore formation: no
confidence: 100

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	sampling date	latitude	longitude
8398	soil of salt mines	Perm region, Berezniki	Russia	RUS	Europe
67772	Soil of salt mines	Perm Krai, Berezniki	Russia	RUS	Europe	2001	59.4167	56.7833

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Environmental	#Terrestrial	#Soil
#Condition	#Saline

taxonmaps

@ref: 69479
File name: preview.99_6922.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_2686;97_3652;98_4620;99_6922&stattab=map
Last taxonomy: Salinicola
16S sequence: DQ979342
Sequence Identity:
Total samples: 220
soil counts: 47
aquatic counts: 98
animal counts: 71
plant counts: 4

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
8398	1	Risk group (German classification)
67772	1

Sequence information

16S sequences

@ref: 8398
description: Salinicola socius strain SMB35 16S ribosomal RNA gene, partial sequence
accession: DQ979342
length: 1433
database: nuccore
NCBI tax ID: 404433

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Salinicola socius DSM 19940	GCA_003206115	scaffold	ncbi	404433
66792	Salinicola socius strain DSM 19940	404433.6	wgs	patric	404433
66792	Salinicola socius DSM 19940	2894301683	draft	img	404433
67772	Salinicola socius SMB35	GCA_001937195	contig	ncbi	404433

GC content

@ref: 8398
GC-content: 63.0
method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@ref	trait	model	description	prediction	confidence	training_data
69481	spore-forming	spore-forming	Ability to form endo- or exospores	no	100	no
69480	gram-positive	gram-positive	Positive reaction to Gram-staining	no	99.969	no
69480	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	no	99.041	no
69480	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	yes	84.256	no
69480	spore-forming	spore-forming	Ability to form endo- or exospores	no	88.082	no
69480	thermophilic	thermophile	Ability to grow at temperatures above or equal to 45°C	no	98.478	yes
69480	flagellated	motile2+	Ability to perform flagellated movement	yes	78.208	no

External links

@ref: 8398

culture collection no.: DSM 19940, VKM B-2397, UCCCB107

straininfo link

@ref: 75568
straininfo: 360154

literature

topic	Pubmed-ID	title	authors	journal	year	mesh	topic2	DOI
Phylogeny	17633412	[Salinicola socius gen. nov., sp. nov., a moderately halophilic bacterium from a naphthalene-utilizing microbial association].	Anan'ina LN, Plotnikova EG, Gavrish EIu, Demakov VA, Evtushenko LI	Mikrobiologiia	2007	Base Composition, Culture Media, Geologic Sediments/microbiology, Halomonadaceae/chemistry/classification/physiology, Naphthalenes/*metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Russia, Sequence Homology, Species Specificity	Cultivation
Phylogeny	19661506	Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and Salinicola halophilus nom. nov., respectively.	de la Haba RR, Sanchez-Porro C, Marquez MC, Ventosa A	Int J Syst Evol Microbiol	2009	Algorithms, Bacterial Typing Techniques, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Halomonadaceae/classification/genetics/physiology, Halomonas/classification/genetics/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, Species Specificity	Genetics	10.1099/ijs.0.014480-0
Phylogeny	23117446	Salinicola zeshunii sp. nov., a moderately halophilic bacterium isolated from soil of a chicken farm.	Cao L, Yan Q, Ni H, Hu G, Hong Q, Li S	Curr Microbiol	2012	Animals, Bacterial Typing Techniques, Base Composition, Chickens, China, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Halomonadaceae/classification/genetics/isolation & purification/physiology, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology	Genetics	10.1007/s00284-012-0259-4
Phylogeny	25944083	Comparative 16S rRNA signatures and multilocus sequence analysis for the genus Salinicola and description of Salinicola acroporae sp. nov., isolated from coral Acropora digitifera.	Lepcha RT, Poddar A, Schumann P, Das SK	Antonie Van Leeuwenhoek	2015	Aerobiosis, Animals, Anthozoa/microbiology, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Halomonadaceae/classification/genetics/isolation & purification/physiology, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Multilocus Sequence Typing/methods, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/*genetics, RNA, Ribosomal, 23S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature	Transcriptome	10.1007/s10482-015-0464-9
Genetics	28729898	Draft genome sequences of strains Salinicola socius SMB35(T), Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia.	Olsson BE, Korsakova ES, Anan'ina LN, Pyankova AA, Mavrodi OV, Plotnikova EG, Mavrodi DV	Stand Genomic Sci	2017			10.1186/s40793-017-0251-5

Reference

@id	authors	catalogue	doi/url	title
8398	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19940)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-19940
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)
67772	Curators of the UCCCB		https://ucccb.uc.pt/
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)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
75568	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID360154.1	StrainInfo: A central database for resolving microbial strain identifiers