Strain identifier

BacDive ID: 24748

Type strain: Yes

Species: Amorphus suaedae

Strain Designation: YC6899

Strain history: <- Y. R. Chung, Gyeongsang Natl. Univ. (GNU), Jinju, Korea; YC6899 <- F. Bibi

NCBI tax ID(s): 1327753 (species)

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General

@ref: 21178

BacDive-ID: 24748

DSM-Number: 23349

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

description: Amorphus suaedae YC6899 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from root of the halophyte Suaedae maritima collected from a tidal flat area.

NCBI tax id

  • NCBI tax id: 1327753
  • Matching level: species

strain history

  • @ref: 21178
  • history: <- Y. R. Chung, Gyeongsang Natl. Univ. (GNU), Jinju, Korea; YC6899 <- F. Bibi

doi: 10.13145/bacdive24748.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Amorphaceae
  • genus: Amorphus
  • species: Amorphus suaedae
  • full scientific name: Amorphus suaedae Hwang et al. 2013

@ref: 21178

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Amorphaceae

genus: Amorphus

species: Amorphus suaedae

full scientific name: Amorphus suaedae Hwang et al. 2013

strain designation: YC6899

type strain: yes

Morphology

cell morphology

  • @ref: 30986
  • gram stain: negative
  • cell length: 1.85 µm
  • cell width: 0.85 µm
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 30986
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21178
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21178positivegrowth28mesophilic
30986positivegrowth12-40
30986positiveoptimum31mesophilic

culture pH

@refabilitytypepHPH range
30986positivegrowth5.0-10.5alkaliphile
30986positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

  • @ref: 30986
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30986
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30986NaClpositivegrowth0-10 %
30986NaClpositiveoptimum3 %

observation

  • @ref: 30986
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3098616449alanine+carbon source
3098622653asparagine+carbon source
3098635391aspartate+carbon source
3098617057cellobiose+carbon source
3098616947citrate+carbon source
3098623652dextrin+carbon source
3098633984fucose+carbon source
3098628260galactose+carbon source
3098617234glucose+carbon source
3098632323glucuronamide+carbon source
3098629987glutamate+carbon source
3098628087glycogen+carbon source
3098651850methyl pyruvate+carbon source
3098617822serine+carbon source
3098630911sorbitol+carbon source
3098630031succinate+carbon source

enzymes

@refvalueactivityec
30986acid phosphatase+3.1.3.2
30986alkaline phosphatase+3.1.3.1
30986catalase+1.11.1.6
30986urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 21178
  • sample type: root of the halophyte Suaedae maritima collected from a tidal flat area
  • host species: Suaeda maritima
  • geographic location: Namhae Island
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Tidal flat
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_34507.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_2498;97_20366;98_25477;99_34507&stattab=map
  • Last taxonomy: Amorphus suaedae subclade
  • 16S sequence: KC006961
  • Sequence Identity:
  • Total samples: 1950
  • soil counts: 153
  • aquatic counts: 1666
  • animal counts: 95
  • plant counts: 36

Safety information

risk assessment

  • @ref: 21178
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21178
  • description: Amorphus suaedae strain YC6899 16S ribosomal RNA gene, partial sequence
  • accession: KC006961
  • length: 1452
  • database: ena
  • NCBI tax ID: 1327753

GC content

@refGC-contentmethod
2117861.3fluorimetric
3098661.3

External links

@ref: 21178

culture collection no.: DSM 23349, KACC 14912, NBRC 107845

straininfo link

  • @ref: 88576
  • straininfo: 399989

literature

  • topic: Phylogeny
  • Pubmed-ID: 23687061
  • title: Amorphus suaedae sp. nov., isolated from the root of a tidal flat plant, Suaeda maritima.
  • authors: Hwang JM, Chung EJ, Park JA, Jeong JH, Jeon CO, Chung YR
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.048959-0
  • year: 2013
  • mesh: Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, Ubiquinone/analysis
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21178Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-23349Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23349)
30986Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172731628776041
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/
88576Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399989.1