Archive BacDiveID:10.13145/bacdive3997.20230509.8.1

Strain identifier

BacDive ID: 3997

Type strain:

Species: Desulfoluna spongiiphila

Strain Designation: AA1

Strain history: <- M. M. Häggblom, Rutgers, State Univ. New Jersey, New Brunswick, USA; AA1 <- Y.-B. Ahn {2004}

NCBI tax ID(s): 419481 (species)

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

General

@ref: 7124

BacDive-ID: 3997

DSM-Number: 17682

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

description: Desulfoluna spongiiphila AA1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from Aplysina aerophoba sponges.

NCBI tax id

NCBI tax id: 419481
Matching level: species

strain history

@ref: 7124
history: <- M. M. Häggblom, Rutgers, State Univ. New Jersey, New Brunswick, USA; AA1 <- Y.-B. Ahn {2004}

doi: 10.13145/bacdive3997.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Deltaproteobacteria
order: Desulfobacterales
family: Desulfobacteraceae
genus: Desulfoluna
species: Desulfoluna spongiiphila
full scientific name: Desulfoluna spongiiphila Ahn et al. 2009

@ref: 7124

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Desulfobacterales

family: Desulfobacteraceae

genus: Desulfoluna

species: Desulfoluna spongiiphila

full scientific name: Desulfoluna spongiiphila Ahn et al. 2009

strain designation: AA1

type strain: yes

Morphology

cell morphology

@ref: 29086
gram stain: negative
cell length: 3 µm
cell width: 1 µm
cell shape: rod-shaped
motility: no

Culture and growth conditions

culture medium

@ref: 7124
name: MARINE DESULFOVIBRIO COMPLEX MEDIUM (DSMZ Medium 1040)
growth: yes
link: https://mediadive.dsmz.de/medium/1040
composition: Name: MARIDESULFOVIBRIO MEDIUM (DSMZ Medium 1040; with strain-specific modifications) Composition: Sea Salt 34.9301 g/l Yeast extract 0.998004 g/l Na2CO3 0.998004 g/l Na-DL-lactate 0.598802 g/l Na2S x 9 H2O 0.299401 g/l MgSO4 x 7 H2O 0.0299401 g/l NaCl 0.00998004 g/l MnSO4 x H2O 0.00499002 g/l (NH4)2Ni(SO4)2 x 6 H2O 0.00279441 g/l CoCl2 x 6 H2O 0.00179641 g/l ZnSO4 x 7 H2O 0.00179641 g/l CaCl2 x 2 H2O 0.000998004 g/l FeSO4 x 7 H2O 0.000998004 g/l Sodium resazurin 0.000499002 g/l AlK(SO4)2 x 12 H2O 0.000179641 g/l CuSO4 x 5 H2O 9.98004e-05 g/l H3BO3 9.98004e-05 g/l Na2MoO4 x 2 H2O 9.98004e-05 g/l Na2WO4 x 2 H2O 9.98004e-05 g/l Na2SeO4 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l Vitamin B12 9.98004e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
7124	positive	growth	28	mesophilic
29086	positive	growth	20-37
29086	positive	optimum	28	mesophilic

culture pH

@ref	ability	type	pH
29086	positive	growth	07-08
29086	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance
7124	anaerobe
29086	anaerobe

spore formation

@ref: 29086
spore formation: no

halophily

@ref: 29086
salt: NaCl
growth: positive
tested relation: optimum
concentration: 2.5 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29086	16947	citrate	+	carbon source
29086	17234	glucose	+	carbon source
29086	24996	lactate	+	carbon source
29086	17272	propionate	+	carbon source
29086	15361	pyruvate	+	carbon source
29086	30031	succinate	+	carbon source

metabolite production

@ref: 29086
Chebi-ID: 16136
metabolite: hydrogen sulfide
production: yes

Isolation, sampling and environmental information

isolation

@ref: 7124
sample type: Aplysina aerophoba sponges
host species: Aplysina aerophoba
geographic location: Mediterranean Sea at the Marine Biological Station of Banyuls-sur-Mer
country: France
origin.country: FRA
continent: Europe

isolation source categories

Cat1: #Host
Cat2: #Invertebrates (Other)
Cat3: #Porifera (Sponges)

taxonmaps

@ref: 69479
File name: preview.99_170428.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_705;96_3816;97_13850;98_63796;99_170428&stattab=map
Last taxonomy: Desulfoluna spongiiphila subclade
16S sequence: EF187256
Sequence Identity:
Total samples: 90
soil counts: 1
aquatic counts: 83
animal counts: 6

Safety information

risk assessment

@ref: 7124
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
29086	Desulfoluna spongiiphila strain AA1 16S ribosomal RNA, partial sequence	EF187256.	1552	nuccore	419481
7124	Desulfoluna spongiiphila strain AA1 16S ribosomal RNA gene, complete sequence	EF187256	1552	ena	419481

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Desulfoluna spongiiphila AA1	GCA_900101345	scaffold	ncbi	419481
66792	Desulfoluna spongiiphila AA1	2654587882	draft	img	419481

GC content

@ref	GC-content	method
7124	58.5	high performance liquid chromatography (HPLC)
29086	58.5
7124	57.2	sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	yes	70.678	yes
flagellated	no	59.053	no
gram-positive	no	98.473	yes
anaerobic	yes	96.176	yes
aerobic	no	92.158	yes
halophile	no	57.576	no
spore-forming	no	88.973	yes
glucose-ferment	no	83.711	no
thermophile	no	99.781	yes
glucose-util	yes	70.076	no

External links

@ref: 7124

culture collection no.: DSM 17682, ATCC BAA 1256

straininfo link

@ref: 73502
straininfo: 403633

literature

topic: Phylogeny
Pubmed-ID: 19605712
title: Desulfoluna spongiiphila sp. nov., a dehalogenating bacterium in the Desulfobacteraceae from the marine sponge Aplysina aerophoba.
authors: Ahn YB, Kerkhof LJ, Haggblom MM
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.005884-0
year: 2009
mesh: Anaerobiosis, Animals, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deltaproteobacteria/*classification/genetics/*isolation & purification/physiology, Fatty Acids/analysis, Halogens/*metabolism, Hydrogen-Ion Concentration, Mediterranean Sea, Molecular Sequence Data, Phenols/*metabolism, Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Sulfates/metabolism, Temperature
topic2: Metabolism

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
7124	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17682)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-17682
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
29086	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	25515	28776041
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		33211880	Nucleic Acids Res. 49: D498-D508 2020
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
73502	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID403633.1	StrainInfo: A central database for resolving microbial strain identifiers