Strain identifier

BacDive ID: 158620

Type strain: Yes

Species: Sandarakinorhabdus cyanobacteriorum

Strain Designation: TH057

NCBI tax ID(s): 1981098 (species)

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General

@ref: 65344

BacDive-ID: 158620

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

description: Sandarakinorhabdus cyanobacteriorum TH057 is a Gram-negative, motile, rod-shaped bacterium that was isolated from cyanobacterial aggregate in eutrophic Lake.

NCBI tax id

  • NCBI tax id: 1981098
  • Matching level: species

doi: 10.13145/bacdive158620.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingosinicellaceae
  • genus: Sandarakinorhabdus
  • species: Sandarakinorhabdus cyanobacteriorum
  • full scientific name: Sandarakinorhabdus cyanobacteriorum Cai et al. 2018

@ref: 65344

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sandarakinorhabdus

species: Sandarakinorhabdus cyanobacteriorum

strain designation: TH057

type strain: yes

Morphology

cell morphology

  • @ref: 65344
  • gram stain: negative
  • cell length: 1.8-2.2 µm
  • cell width: 0.6-1 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 65344
  • colony color: light orange
  • incubation period: 1 day
  • medium used: R2A

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
65344positivegrowth20-37
65344positiveoptimum30mesophilic

culture pH

@refabilitytypepHPH range
65344positivegrowth5-9alkaliphile
65344positiveoptimum7

Physiology and metabolism

halophily

  • @ref: 65344
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-0.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6534430089acetate+assimilation
6534417128adipate-assimilation
6534415956biotin-required for growth
6534417968butyrate-assimilation
6534427689decanoate-assimilation
65344casein-hydrolysis
6534417108D-arabinose+builds acid from
6534415824D-fructose+builds acid from
6534417634D-glucose+builds acid from
6534416899D-mannitol-assimilation
6534416899D-mannitol+builds acid from
6534416024D-mannose-assimilation
6534416024D-mannose+builds acid from
6534417924D-sorbitol+builds acid from
653444853esculin+assimilation
653444853esculin+hydrolysis
6534428757fructose+assimilation
653445291gelatin-assimilation
653445291gelatin-hydrolysis
6534417234glucose-assimilation
6534417754glycerol+builds acid from
6534430849L-arabinose-assimilation
6534417266L-sorbose+builds acid from
6534417716lactose+assimilation
6534425115malate-assimilation
6534417306maltose-assimilation
6534417306maltose+builds acid from
65344506227N-acetylglucosamine-assimilation
65344506227N-acetylglucosamine+builds acid from
6534417632nitrate-reduction
6534416301nitrite-reduction
6534417309pectin-hydrolysis
6534418401phenylacetate-assimilation
6534432032potassium gluconate-assimilation
6534453258sodium citrate-assimilation
6534453426tween 80-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6534415688acetoinno
6534435581indoleno

metabolite tests

  • @ref: 65344
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
65344catalase+1.11.1.6
65344cytochrome oxidase+1.9.3.1
65344alkaline phosphatase+3.1.3.1
65344acid phosphatase+3.1.3.2
65344esterase (C 4)+
65344esterase Lipase (C 8)+
65344leucine arylamidase+3.4.11.1
65344valine arylamidase+
65344cystine arylamidase+3.4.11.3
65344alpha-chymotrypsin+3.4.21.1
65344naphthol-AS-BI-phosphohydrolase+
65344beta-galactosidase+3.2.1.23

Isolation, sampling and environmental information

isolation

  • @ref: 65344
  • sample type: cyanobacterial aggregate in eutrophic Lake
  • geographic location: Lake Taihu
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 31.5
  • longitude: 120.183
  • enrichment culture: R2A
  • enrichment culture temperature: 30
  • isolation procedure: Cyanobacterial aggregates were collected and transferred to 500ml beakers and left at room temperature for 2h. This resulted in floatation of the cyanobacterial aggregates to the top of the beaker. Several of the largest aggregates were selected for testing and washed three times in autoclaved lake water. The washed aggregates were then mixed with sterile sand followed by vortexing for 60s. Suspended cells were then serially diluted and the dilutions were plated on R2A agar plates and then incub

isolation source categories

Cat1Cat2Cat3
#Host#Microbial#Bacteria
#Environmental#Aquatic#Lake (large)

taxonmaps

  • @ref: 69479
  • File name: preview.99_75743.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_620;97_40649;98_52971;99_75743&stattab=map
  • Last taxonomy: Sandarakinorhabdus cyanobacteriorum subclade
  • 16S sequence: MG519281
  • Sequence Identity:
  • Total samples: 3421
  • soil counts: 449
  • aquatic counts: 2448
  • animal counts: 350
  • plant counts: 174

Sequence information

16S sequences

  • @ref: 65344
  • description: 16S rRNA gene sequence
  • accession: MG519281
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sandarakinorhabdus cyanobacteriorum TH057GCA_002251755scaffoldncbi1981098
66792Sandarakinorhabdus cyanobacteriorum TH0572826983331completeimg1981098

GC content

  • @ref: 65344
  • GC-content: 66.1
  • method: genome sequence analysis

External links

@ref: 65344

culture collection no.: CGMCC 1.15803, LMG 30294

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29458469Sandarakinorhabdus cyanobacteriorum sp. nov., a novel bacterium isolated from cyanobacterial aggregates in a eutrophic lake.Cai H, Cui H, Zeng Y, An M, Jiang HInt J Syst Evol Microbiol10.1099/ijsem.0.0025712018Bacterial Typing Techniques, Base Composition, China, Cyanobacteria, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny33629948Sandarakinorhabdus rubra sp. nov., and Sandarakinorhabdus oryzae sp. nov., isolated from oxidized rice paddy soil.Cho GY, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0047222021

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
65344Haiyuan Cai, Henglin Cui, Yonghui Zeng, Mingli An, Helong JiangSandarakinorhabdus cyanobacteriorum sp. nov., a novel bacterium isolated from cyanobacterial aggregates in a eutrophic lake10.1099/ijsem.0.002571IJSEM 68: 730-735 201829458469
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/