Strain identifier

BacDive ID: 140806

Type strain: Yes

Species: Rhodobacter sediminis

Strain Designation: N1

Strain history: S.-S. Lee; KEMB, Kyonggi Univ., South Korea; N1.

NCBI tax ID(s): 1783356 (species)

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General

@ref: 43590

BacDive-ID: 140806

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

description: Rhodobacter sediminis N1 is an aerobe, Gram-negative, motile bacterium that was isolated from laggon sediment near North Carolina Central University.

NCBI tax id

  • NCBI tax id: 1783356
  • Matching level: species

strain history

  • @ref: 67770
  • history: S.-S. Lee; KEMB, Kyonggi Univ., South Korea; N1.

doi: 10.13145/bacdive140806.20230509.8.1

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 sediminis
  • full scientific name: Rhodobacter sediminis Subhash and Lee 2016

@ref: 43590

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Rhodobacter

species: Rhodobacter sediminis

strain designation: N1

type strain: yes

Morphology

cell morphology

  • @ref: 43590
  • gram stain: negative
  • cell length: 2.1-4 µm
  • cell width: 0.5-0.7 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 43590
  • colony color: Reddish-brown
  • medium used: Basal medium

Culture and growth conditions

culture medium

  • @ref: 43590
  • name: Basal medium
  • growth: yes
  • composition: sodium pyruvate (0.3 %, w/v), yeast extract (0.3 %, w/v), Casamino acids (0.001 %, w/v) and ammonium chloride (0.01 %, w/v)

culture temp

@refgrowthtypetemperaturerange
43590positivegrowth12-45
43590positiveoptimum27-35mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43590positivegrowth6-9alkaliphile
43590positiveoptimum6.5-8

Physiology and metabolism

oxygen tolerance

  • @ref: 43590
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43590NaClpositivegrowth0-3.5 %(w/v)
43590NaClpositiveoptimum0-0.5 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4359017057cellobiose-builds acid from
4359017634D-glucose-builds acid from
4359062345L-rhamnose-builds acid from
4359028053melibiose-builds acid from
4359016634raffinose-builds acid from
4359017057cellobiose-growth
4359062345L-rhamnose-growth
4359017716lactose-growth
4359016634raffinose-growth
4359017029chitin-hydrolysis
435905291gelatin-hydrolysis
4359053426tween 80-hydrolysis
4359015824D-fructose+builds acid from
4359012936D-galactose+builds acid from
4359016899D-mannitol+builds acid from
4359030849L-arabinose+builds acid from
4359017306maltose+builds acid from
4359017992sucrose+builds acid from
4359035391aspartate+growth
4359015824D-fructose+growth
4359012936D-galactose+growth
4359017634D-glucose+growth
4359016899D-mannitol+growth
4359017924D-sorbitol+growth
4359023652dextrin+growth
4359029985L-glutamate+growth
4359017306maltose+growth
4359015361pyruvate+growth
4359017992sucrose+growth
43590casein+hydrolysis
4359028017starch+hydrolysis
4359053424tween 20+hydrolysis
4359016199urea+hydrolysis
4359033403elemental sulfur+sulfur source
4359016189sulfate+sulfur source
4359016094thiosulfate+sulfur source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
43590100147nalidixic acidyesyes100 µg (disc)
4359017698chloramphenicolyesyes100 µg (disc)
4359028077rifampicinyesyes100 µg (disc)
4359028971ampicillinyesyes100 µg (disc)
4359018208penicillin gyesyes100 µg (disc)

enzymes

@refvalueactivityec
43590esterase (C 4)+
43590esterase Lipase (C 8)+
43590leucine arylamidase+3.4.11.1
43590cystine arylamidase+3.4.11.3
43590acid phosphatase+3.1.3.2
43590naphthol-AS-BI-phosphohydrolase+
43590alpha-glucosidase+3.2.1.20
43590catalase+1.11.1.6
43590cytochrome oxidase+1.9.3.1
43590alkaline phosphatase-3.1.3.1
43590lipase (C 14)-
43590valine arylamidase-
43590trypsin-3.4.21.4
43590alpha-chymotrypsin-3.4.21.1
43590alpha-galactosidase-3.2.1.22
43590beta-galactosidase-3.2.1.23
43590beta-glucuronidase-3.2.1.31
43590beta-glucosidase-3.2.1.21
43590N-acetyl-beta-glucosaminidase-3.2.1.52
43590alpha-mannosidase-3.2.1.24
43590alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43590laggon sediment near North Carolina Central UniversityNorth CarolinaUSAUSANorth America
67770Lagoon sediments near North Carolina Central Univ.NCUSAUSANorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_2602.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1054;97_1659;98_2016;99_2602&stattab=map
  • Last taxonomy: Rhodobacter
  • 16S sequence: LT009496
  • Sequence Identity:
  • Total samples: 18101
  • soil counts: 1824
  • aquatic counts: 12158
  • animal counts: 3470
  • plant counts: 649

Sequence information

16S sequences

  • @ref: 43590
  • description: 16S rRNA gene sequence
  • accession: LT009496
  • database: nuccore

GC content

@refGC-contentmethod
4359070.8high performance liquid chromatography (HPLC)
6777069.6-71.6high performance liquid chromatography (HPLC)

External links

@ref: 43590

culture collection no.: KEMB 563-471, JCM 31175

literature

  • topic: Phylogeny
  • Pubmed-ID: 27150292
  • title: Rhodobacter sediminis sp. nov., isolated from lagoon sediments.
  • authors: Subhash Y, Lee SS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001130
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, North Carolina, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacter/*classification/genetics/isolation & purification, Sequence Analysis, DNA, *Water Microbiology
  • topic2: Transcriptome

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
43590Y. Subhash, Sang-Seob LeeRhodobacter sediminis sp. nov., isolated from lagoon sediments10.1099/ijsem.0.001130IJSEM 66: 2965-2970 201627150292
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/