Archive BacDiveID:10.13145/bacdive13791.20230509.8.1

Strain identifier

BacDive ID: 13791

Type strain:

Species: Sulfitobacter pontiacus

Strain history: <- DSM <- D Y Sorokin, CHLG 10

NCBI tax ID(s): 60137 (species)

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

General

@ref: 3777

BacDive-ID: 13791

DSM-Number: 10014

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

description: Sulfitobacter pontiacus DSM 10014 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from O2 : H2S interface water.

NCBI tax id

NCBI tax id: 60137
Matching level: species

strain history

@ref	history
3777	<- D. Y. Sorokin
67770	IAM 15344 <-- DSM 10014 <-- D. Y. Sorokin CHLG 10.
67771	<- DSM <- D Y Sorokin, CHLG 10

doi: 10.13145/bacdive13791.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Rhodobacterales
family: Roseobacteraceae
genus: Sulfitobacter
species: Sulfitobacter pontiacus
full scientific name: Sulfitobacter pontiacus Sorokin 1996

@ref: 3777

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Sulfitobacter

species: Sulfitobacter pontiacus

full scientific name: Sulfitobacter pontiacus Sorokin 1996

type strain: yes

Morphology

cell morphology

@ref: 67771
gram stain: negative

Culture and growth conditions

culture medium

@ref: 3777
name: SULFITOBACTER PONTIACUS MEDIUM (DSMZ Medium 733)
growth: yes
link: https://mediadive.dsmz.de/medium/733
composition: Name: SULFITOBACTER PONTIACUS MEDIUM (DSMZ Medium 733) Composition: HEPES 7.99201 g/l Na-acetate 1.64068 g/l Yeast extract 0.999001 g/l K2HPO4 0.999001 g/l NH4Cl 0.499501 g/l Peptone 0.499501 g/l Biotin 0.0999001 g/l MgSO4 x 7 H2O 0.002997 g/l Nitrilotriacetic acid 0.0014985 g/l NaCl 0.000999001 g/l MnSO4 x H2O 0.0004995 g/l CoSO4 x 7 H2O 0.00017982 g/l ZnSO4 x 7 H2O 0.00017982 g/l FeSO4 x 7 H2O 9.99001e-05 g/l CaCl2 x 2 H2O 9.99001e-05 g/l NiCl2 x 6 H2O 2.997e-05 g/l AlK(SO4)2 x 12 H2O 1.998e-05 g/l Na2MoO4 x 2 H2O 9.99001e-06 g/l H3BO3 9.99001e-06 g/l CuSO4 x 5 H2O 9.99001e-06 g/l Na2WO4 x 2 H2O 3.996e-07 g/l Na2SeO3 x 5 H2O 2.997e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
3777	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Physiology and metabolism

oxygen tolerance

@ref: 67771
oxygen tolerance: aerobe

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
3777	O₂ : H₂S interface water	Black Sea	Russia	RUS	Europe
67770	O₂:H₂S interface water	Black Sea	Russia	RUS
67771	From O2 : H2S interface water; Russia	Black Sea	Russia	RUS	Asia

isolation source categories

Cat1	Cat2
#Environmental	#Aquatic
#Condition	#Sulfuric

taxonmaps

@ref: 69479
File name: preview.99_3348.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_252;97_275;98_306;99_3348&stattab=map
Last taxonomy: Sulfitobacter pontiacus
16S sequence: Y13155
Sequence Identity:
Total samples: 2001
soil counts: 26
aquatic counts: 1830
animal counts: 141
plant counts: 4

Safety information

risk assessment

@ref: 3777
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Sulfitobacter pontiacus 16S rRNA gene, partial	Y13155	1397	ena	60137
20218	Sulfitobacter pontiacus strain LMG19752 16S ribosomal RNA gene, partial sequence	DQ915637	1305	ena	60137

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Sulfitobacter pontiacus strain DSM 10014	60137.10	wgs	patric	60137
66792	Sulfitobacter pontiacus DSM 10014	2622736431	draft	img	60137
67770	Sulfitobacter pontiacus DSM 10014	GCA_900106935	scaffold	ncbi	60137

GC content

@ref: 67770
GC-content: 62.1
method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
gram-positive	no	97.893	yes
anaerobic	no	98.22	yes
halophile	yes	91.131	no
spore-forming	no	96.764	no
glucose-util	yes	76.284	no
thermophile	no	98.429	yes
flagellated	no	84.1	no
aerobic	yes	95.155	no
motile	yes	67.28	no
glucose-ferment	no	91.015	no

External links

@ref: 3777

culture collection no.: DSM 10014, CHLG 10, KCTC 32185, LMD 95.85, JCM 21789, IAM 15344, LMG 19752, NCCB 95085, VKM B-2022

straininfo link

@ref: 82969
straininfo: 14630

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	10319472	Sulfitobacter mediterraneus sp. nov., a new sulfite-oxidizing member of the alpha-Proteobacteria.	Pukall R, Buntefuss D, Fruhling A, Rohde M, Kroppenstedt RM, Burghardt J, Lebaron P, Bernard L, Stackebrandt E	Int J Syst Bacteriol	10.1099/00207713-49-2-513	1999	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gram-Negative Aerobic Rods and Cocci/classification/genetics/isolation & purification/physiology, Mediterranean Sea, Molecular Sequence Data, Nucleic Acid Hybridization, Oligonucleotide Probes, Oxidation-Reduction, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Species Specificity, Sulfites/metabolism, Water Microbiology	Genetics
Phylogeny	17392188	Sulfitobacter litoralis sp. nov., a marine bacterium isolated from the East Sea, Korea.	Park JR, Bae JW, Nam YD, Chang HW, Kwon HY, Quan ZX, Park YH	Int J Syst Evol Microbiol	10.1099/ijs.0.64267-0	2007	DNA, Bacterial, DNA, Ribosomal/genetics, Genes, Bacterial, Genes, rRNA, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics, Seawater/microbiology	Genetics
Phylogeny	26971334	Paradonghicola geojensis gen. nov., sp. nov., isolated from seawater, Geoje-si, South Korea.	Lee K, Srinivasan S, Lee SS	Arch Microbiol	10.1007/s00203-015-1182-4	2016	Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Typing, Phosphatidylethanolamines/analysis, Phosphatidylglycerols/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysis	Transcriptome
Phylogeny	28184991	Sulfitobacter pontiacus subsp. fungiae subsp. nov., Isolated from Coral Fungia seychellensis from Andaman Sea, and Description of Sulfitobacter pontiacus subsp. pontiacus subsp. nov.	Zachariah S, Kumari P, Das SK	Curr Microbiol	10.1007/s00284-017-1200-7	2017	Animals, Anthozoa/microbiology, Base Composition/genetics, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Gram-Negative Aerobic Bacteria/classification/genetics, Rhodobacteraceae/classification/genetics
Phylogeny	33655407	Sulfitobacter algicola sp. nov., isolated from green algae.	Wang CN, Liu Y, Wang J, Du ZJ, Wang MY	Arch Microbiol	10.1007/s00203-021-02213-w	2021	Bacterial Typing Techniques, Base Composition, China, Chlorophyta/microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/genetics, Phospholipids/chemistry, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
3777	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10014)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-10014
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
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)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
67771	Curators of the KCTC		https://kctc.kribb.re.kr/En/Kctc
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
82969	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID14630.1	StrainInfo: A central database for resolving microbial strain identifiers