Strain identifier

BacDive ID: 13823

Type strain: Yes

Species: Rhodobacter aestuarii

Strain Designation: JA296

Strain history: <- C. Sasikala, Centre Environment, Inst. Sci. and Technol., J. N. T. Univ., Hyderabad, India; JA296 <- P. A. Kumar

NCBI tax ID(s): 453582 (species)

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General

@ref: 8402

BacDive-ID: 13823

DSM-Number: 19945

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

description: Rhodobacter aestuarii JA296 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from brown-coloured microbial mat from brackish water of mangrove forest.

NCBI tax id

  • NCBI tax id: 453582
  • Matching level: species

strain history

  • @ref: 8402
  • history: <- C. Sasikala, Centre Environment, Inst. Sci. and Technol., J. N. T. Univ., Hyderabad, India; JA296 <- P. A. Kumar

doi: 10.13145/bacdive13823.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Rhodobacter
  • species: Rhodobacter aestuarii
  • full scientific name: Rhodobacter aestuarii Venkata Ramana et al. 2009

@ref: 8402

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Rhodobacter

species: Rhodobacter aestuarii

full scientific name: Rhodobacter aestuarii Venkata Ramana et al. 2009

strain designation: JA296

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29034negative1.75 µm0.85 µmrod-shapedyes
69480negative99.994

pigmentation

  • @ref: 29034
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29034positivegrowth25-30mesophilic
29034positiveoptimum30mesophilic
60471positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29034positivegrowth6-8.5alkaliphile
29034positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29034anaerobe
60471aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.986

halophily

  • @ref: 29034
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <2 %

observation

  • @ref: 29034
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2903424996lactate+carbon source
2903415361pyruvate+carbon source

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
8402brown-coloured microbial mat from brackish water of mangrove forestDangmal, BhitarkanikaIndiaINDAsia
60471Mud from microbial mat of mangrove forestOrissa,Bhitarkanika,DangmalIndiaINDAsia2007-05-15

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Brackish
#Environmental#Aquatic#Mangrove
#Environmental#Microbial community#Microbial mat
#Environmental#Terrestrial#Forest

taxonmaps

  • @ref: 69479
  • File name: preview.99_11884.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1054;97_1232;98_4017;99_11884&stattab=map
  • Last taxonomy: Rhodobacter aestuarii subclade
  • 16S sequence: AM748926
  • Sequence Identity:
  • Total samples: 5
  • soil counts: 1
  • aquatic counts: 4

Safety information

risk assessment

  • @ref: 8402
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8402
  • description: Rhodobacter aestuarii partial 16S rRNA gene, type strain JA296T
  • accession: AM748926
  • length: 1369
  • database: ena
  • NCBI tax ID: 453582

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodobacter aestuarii DSM 19945GCA_900156655contigncbi453582
66792Rhodobacter aestuarii JA296GCA_003053525scaffoldncbi453582
66792Rhodobacter aestuarii strain DSM 19945453582.3wgspatric453582
66792Rhodobacter aestuarii JA2962740891822draftimg453582
66792Rhodobacter aestuarii DSM 199452681813516draftimg453582

GC content

@refGC-contentmethod
840265.1high performance liquid chromatography (HPLC)
2903465.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno76.964no
gram-positiveno98.718no
anaerobicno74.941no
halophileno73.137no
spore-formingno96.046no
thermophileno95.979yes
glucose-utilyes81.353no
aerobicno87.773no
motileyes63.105no
glucose-fermentno86.136no

External links

@ref: 8402

culture collection no.: DSM 19945, CCUG 55130, JCM 14887

straininfo link

  • @ref: 83000
  • straininfo: 409841

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19406806Rhodobacter aestuarii sp. nov., a phototrophic alphaproteobacterium isolated from an estuarine environment.Venkata Ramana V, Anil Kumar P, Srinivas TN, Sasikala Ch, Ramana ChVInt J Syst Evol Microbiol10.1099/ijs.0.004507-02009Bacterial Typing Techniques, Bacteriochlorophyll A/metabolism, Carotenoids/metabolism, DNA, Bacterial/analysis, Fatty Acids/analysis, Fresh Water/*microbiology, India, Molecular Sequence Data, Phenotype, *Phototrophic Processes, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizophoraceae, Rhodobacter/*classification/genetics/isolation & purification/physiology, Sequence Analysis, DNA, Species Specificity, TreesMetabolism
Phylogeny22389279Rhodobacter viridis sp. nov., a phototrophic bacterium isolated from mud of a stream.Raj PS, Ramaprasad EVV, Vaseef S, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.038471-02012Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Carotenoids/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacter/*classification/genetics/isolation & purification, Rivers/*microbiology, Sequence Analysis, DNA, *Water MicrobiologyGenetics
Phylogeny24135316Paenirhodobacter enshiensis gen. nov., sp. nov., a non-photosynthetic bacterium isolated from soil, and emended descriptions of the genera Rhodobacter and Haematobacter.Wang D, Liu H, Zheng S, Wang GInt J Syst Evol Microbiol10.1099/ijs.0.050351-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacter/classification, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny32589572Frigidibacter oleivorans sp. nov., isolated from a deep well with oil reservoir water.Zhang YX, Li FL, Ma SC, Zheng GD, Chen WF, Li WJ, Wang LInt J Syst Evol Microbiol10.1099/ijsem.0.0042942020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Oil and Gas Fields/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry, WaterTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8402Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19945)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19945
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
29034Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2546428776041
60471Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55130)https://www.ccug.se/strain?id=55130
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)
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
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83000Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID409841.1StrainInfo: A central database for resolving microbial strain identifiers