Strain identifier

BacDive ID: 3924

Type strain: Yes

Species: Dermacoccus abyssi

Strain Designation: MT1.1

Strain history: CIP <- 2006, DSMZ <- W. Pathom-aree, Newcastle Univ., Newcastle upon Tyne, UK: strain MT1.1

NCBI tax ID(s): 322596 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7061

BacDive-ID: 3924

DSM-Number: 17573

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, rod-shaped

description: Dermacoccus abyssi MT1.1 is an aerobe, spore-forming, mesophilic bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 322596
  • Matching level: species

strain history

@refhistory
7061<- W. Pathom-aree; MT1.1
67770NCIMB 14084 <-- W. Pathom-aree MT1.1.
115985CIP <- 2006, DSMZ <- W. Pathom-aree, Newcastle Univ., Newcastle upon Tyne, UK: strain MT1.1

doi: 10.13145/bacdive3924.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermacoccaceae
  • genus: Dermacoccus
  • species: Dermacoccus abyssi
  • full scientific name: Dermacoccus abyssi Pathom-aree et al. 2006

@ref: 7061

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermacoccaceae

genus: Dermacoccus

species: Dermacoccus abyssi

full scientific name: Dermacoccus abyssi Pathom-aree et al. 2006

strain designation: MT1.1

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
31729positive0.8-1.5 µmrod-shapedno
115985positivecoccus-shapedno

colony morphology

@refcolony colorincubation periodmedium used
19750Brown beige (1011)10-14 daysISP 2
1975010-14 daysISP 3
19750Olive yellow (1020)10-14 daysISP 4
19750Brown beige (1011)10-14 daysISP 5
19750Brown beige (1011)10-14 daysISP 6
19750Pearl orange (2013)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19750noISP 2
19750noISP 3
19750noISP 4
19750noISP 5
19750noISP 6
19750noISP 7

pigmentation

  • @ref: 31729
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7061TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
19750ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19750ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19750ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19750ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19750ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19750ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
37506MEDIUM 338 - for Sanguibacter keddieiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (3.000 g);Trypto casein soy agar (30.000 g)
40035MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
115985CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338

culture temp

@refgrowthtypetemperaturerange
19750positiveoptimum28mesophilic
7061positivegrowth28mesophilic
31729positivegrowth10-37
31729positiveoptimum28mesophilic
37506positivegrowth30mesophilic
40035positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31729positivegrowth7
31729positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31729aerobe
115985obligate aerobe

spore formation

  • @ref: 31729
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31729NaClpositivegrowth7.5-10 %
31729NaClpositiveoptimum7.5 %

observation

@refobservation
31729aggregates in chains
67770quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
317294853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11598517632nitrate+reduction
11598516301nitrite-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 115985
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
115985oxidase-
115985catalase+1.11.1.6
115985urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19750---+---------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19750+++++----++---++---
115985-++++--+-++---+-----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
115985-------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountry
7061marine sedimentMariana Trench
67770Sediment from the Challenger Deep of the Mariana Trench
115985Environment, Marine sedimentNorthwest PacificPacific Ocean

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_3622.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_403;97_455;98_524;99_3622&stattab=map
  • Last taxonomy: Dermacoccus
  • 16S sequence: AY894323
  • Sequence Identity:
  • Total samples: 3867
  • soil counts: 94
  • aquatic counts: 315
  • animal counts: 3401
  • plant counts: 57

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70611Risk group (German classification)
197501Risk group (German classification)
1159851Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7061
  • description: Dermacoccus abyssi strain MT1.1 16S ribosomal RNA gene, partial sequence
  • accession: AY894323
  • length: 1469
  • database: ena
  • NCBI tax ID: 322596

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dermacoccus abyssi MT1.12833109367draftimg322596
67770Dermacoccus abyssi MT1.1GCA_003515945contigncbi322596

GC content

@refGC-contentmethod
706165.2
6777065.2high performance liquid chromatography (HPLC)

External links

@ref: 7061

culture collection no.: DSM 17573, CIP 109302, NCIMB 14084, JCM 14339

straininfo link

  • @ref: 73433
  • straininfo: 297165

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738097Dermacoccus abyssi sp. nov., a piezotolerant actinomycete isolated from the Mariana Trench.Pathom-Aree W, Nogi Y, Sutcliffe IC, Ward AC, Horikoshi K, Bull AT, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.64133-02006Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Geologic Sediments/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny17012551Dermacoccus barathri sp. nov. and Dermacoccus profundi sp. nov., novel actinomycetes isolated from deep-sea mud of the Mariana Trench.Pathom-Aree W, Nogi Y, Ward AC, Horikoshi K, Bull AT, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.64250-02006Actinomycetales/chemistry/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Phenotype, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics
Metabolism20448892Dermacozines, a new phenazine family from deep-sea dermacocci isolated from a Mariana Trench sediment.Abdel-Mageed WM, Milne BF, Wagner M, Schumacher M, Sandor P, Pathom-aree W, Goodfellow M, Bull AT, Horikoshi K, Ebel R, Diederich M, Fiedler HP, Jaspars MOrg Biomol Chem10.1039/c001445a2010Actinomycetales/*chemistry/metabolism, Antineoplastic Agents/chemistry/isolation & purification/metabolism/pharmacology, Free Radical Scavengers/chemistry/isolation & purification/metabolism/pharmacology, Geologic Sediments/*chemistry, Humans, Inhibitory Concentration 50, K562 Cells, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Conformation, Pacific Ocean, Phenazines/*chemistry/isolation & purification/metabolism/*pharmacology, PigmentationEnzymology
Metabolism24309230Biodecolorization of a food azo dye by the deep sea Dermacoccus abyssi MT1.1(T) strain from the Mariana Trench.Lang W, Sirisansaneeyakul S, Martins LO, Ngiwsara L, Sakairi N, Pathom-aree W, Okuyama M, Mori H, Kimura AJ Environ Manage10.1016/j.jenvman.2013.11.0022013Actinomycetales/*metabolism, Azo Compounds/*metabolism, Coloring Agents/*metabolism, Kinetics, NADH, NADPH Oxidoreductases/metabolism, Nitroreductases, Pacific Ocean, Water Pollutants, Chemical/*metabolism, Water Pollution, Chemical/*prevention & controlEnzymology
Phylogeny24499261Dermacozines H-J isolated from a deep-sea strain of Dermacoccus abyssi from Mariana Trench sediments.Wagner M, Abdel-Mageed WM, Ebel R, Bull AT, Goodfellow M, Fiedler HP, Jaspars MJ Nat Prod10.1021/np400952d2014Actinomycetales/*chemistry, Biphenyl Compounds/pharmacology, DNA, Bacterial/genetics, Free Radical Scavengers/chemistry/*isolation & purification/pharmacology, Geologic Sediments/chemistry, Inhibitory Concentration 50, Molecular Structure, Nuclear Magnetic Resonance, Biomolecular, Oxidation-Reduction, Phenazines/chemistry/*isolation & purification/pharmacology, Phylogeny, Picrates/pharmacologyEnzymology
Phylogeny32106586Whole Genome Sequence of Dermacoccus abyssi MT1.1 Isolated from the Challenger Deep of the Mariana Trench Reveals Phenazine Biosynthesis Locus and Environmental Adaptation Factors.Abdel-Mageed WM, Juhasz B, Lehri B, Alqahtani AS, Nouioui I, Pech-Puch D, Tabudravu JN, Goodfellow M, Rodriguez J, Jaspars M, Karlyshev AVMar Drugs10.3390/md180301312020Acclimatization, Actinobacteria/*genetics/isolation & purification/metabolism, Animals, Geologic Sediments/microbiology, Oceans and Seas, Phenazines/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Whole Genome SequencingGenetics
Stress35205058Plant Beneficial Deep-Sea Actinobacterium, Dermacoccus abyssi MT1.1(T) Promote Growth of Tomato (Solanum lycopersicum) under Salinity Stress.Rangseekaew P, Barros-Rodriguez A, Pathom-Aree W, Manzanera MBiology (Basel)10.3390/biology110201912022

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7061Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17573)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17573
19750Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM17573.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31729Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2800528776041
37506Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7029
40035Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7138
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69479João 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
73433Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297165.1StrainInfo: A central database for resolving microbial strain identifiers
115985Curators of the CIPCollection of Institut Pasteur (CIP 109302)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109302