Strain identifier

BacDive ID: 13717

Type strain: Yes

Species: Paracoccus alkenifer

Strain Designation: 901/1, A901/1

Strain history: CIP <- 1998, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain A901/1

NCBI tax ID(s): 65735 (species)

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General

@ref: 4237

BacDive-ID: 13717

DSM-Number: 11593

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

description: Paracoccus alkenifer 901/1 is an obligate aerobe, mesophilic bacterium that was isolated from biofilter for waste gas treatment.

NCBI tax id

  • NCBI tax id: 65735
  • Matching level: species

strain history

@refhistory
4237<- A. Lipski, Univ. Osnabrück <- A. Ahrens, Univ. Osnabrück, 901/1
340841998, A. Lipski, Univ. Osnabrück, Germany: strain A901/1
116256CIP <- 1998, A. Lipski, Osnabrück Univ., Osnabrück, Germany: strain A901/1

doi: 10.13145/bacdive13717.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Paracoccus
  • species: Paracoccus alkenifer
  • full scientific name: Paracoccus alkenifer Lipski et al. 1998

@ref: 4237

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus alkenifer

full scientific name: Paracoccus alkenifer Lipski et al. 1998

strain designation: 901/1, A901/1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.907
6948099.997negative
116256yesnegativerod-shaped

colony morphology

  • @ref: 116256

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4237NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
34084MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116256CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4237positivegrowth30mesophilic
34084positivegrowth30mesophilic
116256positivegrowth25-30mesophilic
116256nogrowth5psychrophilic
116256nogrowth10psychrophilic
116256nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116256
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.978

halophily

@refsaltgrowthtested relationconcentration
116256NaClpositivegrowth0-6 %
116256NaClnogrowth8 %
116256NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116256citrate-carbon source16947
116256esculin-hydrolysis4853
116256nitrate+reduction17632
116256nitrite+reduction16301
116256nitrate+respiration17632

antibiotic resistance

  • @ref: 116256
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116256
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116256oxidase+
116256beta-galactosidase-3.2.1.23
116256alcohol dehydrogenase-1.1.1.1
116256gelatinase-
116256amylase-
116256DNase-
116256caseinase-3.4.21.50
116256catalase+1.11.1.6
116256tween esterase-
116256lecithinase-
116256lipase-
116256lysine decarboxylase-4.1.1.18
116256ornithine decarboxylase-4.1.1.17
116256protease-
116256tryptophan deaminase-
116256urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116256-+++-+-----+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116256-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116256-------------------------------------------------------------+-----------+-+--++---+----+-+++++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4237biofilter for waste gas treatmentLingenGermanyDEUEurope
116256Experimental biofilterBrögbern, LingenGermanyDEUEurope1990

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioremediation#Biofilter
#Engineered#Waste#Waste gas

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
42371Risk group (German classification)
1162561Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4237
  • description: Paracoccus alkenifer 16S rRNA gene
  • accession: Y13827
  • length: 1408
  • database: ena
  • NCBI tax ID: 65735

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paracoccus alkenifer DSM 11593GCA_900108405contigncbi65735
66792Paracoccus alkenifer strain DSM 1159365735.6wgspatric65735
66792Paracoccus alkenifer DSM 115932617270733draftimg65735

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno84no
gram-positiveno98.211no
anaerobicno94.863no
halophileno65.192no
spore-formingno96.802no
glucose-utilyes57.169no
thermophileno85.839yes
flagellatedno88.417no
motileno58.214no
aerobicyes75.196no
glucose-fermentno90.72no

External links

@ref: 4237

culture collection no.: DSM 11593, CIP 105684

straininfo link

  • @ref: 82901
  • straininfo: 49143

literature

  • topic: Phylogeny
  • Pubmed-ID: 30489238
  • title: Description of Paracoccus endophyticus sp. nov., isolated from Gastrodia elata Blume.
  • authors: Zhang H, Li YQ, Xiao M, Fang BZ, Alkhalifah DHM, Hozzein WN, Rao MPN, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003142
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrodia/*microbiology, Nucleic Acid Hybridization, Paracoccus/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, Plant Tubers/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitle
4237Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11593)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11593
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
34084Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17730
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)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
82901Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49143.1StrainInfo: A central database for resolving microbial strain identifiers
116256Curators of the CIPCollection of Institut Pasteur (CIP 105684)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105684