Strain identifier

BacDive ID: 159721

Type strain: Yes

Species: Ferrigenium kumadai

Strain Designation: An22

Strain history: T. Watanabe; Grad. Sch. of Bioagric. Sci., Nagoya Univ., Japan; An22.

NCBI tax ID(s): 1682490 (species)

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General

@ref: 66622

BacDive-ID: 159721

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

description: Ferrigenium kumadai An22 is a microaerophile, lithotroph, Gram-negative bacterium that was isolated from soil sample from a paddy field.

NCBI tax id

  • NCBI tax id: 1682490
  • Matching level: species

strain history

  • @ref: 67770
  • history: T. Watanabe; Grad. Sch. of Bioagric. Sci., Nagoya Univ., Japan; An22.

doi: 10.13145/bacdive159721.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Nitrosomonadales
  • family: Gallionellaceae
  • genus: Ferrigenium
  • species: Ferrigenium kumadai
  • full scientific name: Ferrigenium kumadai Khalifa et al. 2018

@ref: 66622

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Nitrosomonadales

family: Gallionellaceae

genus: Ferrigenium

species: Ferrigenium kumadai

strain designation: An22

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
66622negative1.43 µm0.29 µmrod-shapedyes
69480yes98.055
69480negative99.996

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
66622positivegrowth12-37
66622positiveoptimum25-30mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepH
66622positivegrowth5.2-6.8
66622positiveoptimum5.9-6.2

Physiology and metabolism

oxygen tolerance

  • @ref: 66622
  • oxygen tolerance: microaerophile

nutrition type

  • @ref: 66622
  • type: lithotroph

spore formation

@refspore formationconfidence
66622no
69480no99.99
69481no100

halophily

  • @ref: 66622
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 1.46 g/L

observation

@refobservation
66622growing with opposing gradients of Fe(II) and O 2 , and autotrophic via the Calvin-Benson-Bassham cycle as indicated from the presence of ribulose-1,5-bisphosphate carboxylase/oxygenase.
67770quinones: Q-10, Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6662215138sulfide-energy source
6662215361pyruvate-energy source
6662216094thiosulfate-energy source
6662216301nitrite-energy source
6662216411acetic acid-energy source
6662217234glucose-energy source
6662218276dihydrogen-energy source
6662229035manganous ion-energy source
6662253258citric acid-energy source
6662229033ferrous ion+energy source

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment culture durationenrichment culture temperatureisolation procedure
66622soil sample from a paddy field2010-04-13Crop Institute, Aichi Agricultural Research CentreJapanJPNAsia34.9725137.0763-4 weeks25Micro-oxic soil incubation was conducted to form iron oxide-deposited microbial colonies, meaning enrichment of FeOB, on the soil surface [16]. The paddy soil sample was preincubated under flooded and dark conditions in a glass beaker for 3 weeks at 25°C. Then the soil was incubated under anoxic conditions in a test tube (30 mm diameter and 200 mm long) with a sleeve stopper made from synthetic rubber. Because traces of O2 diffused slowly through the stopper (29.2 nmol cm-3 day-1), a microaerobic atmosphere could be established in the tubes. Iron oxide-deposited microbial colonies that formed after 3-4 weeks of incubation were subjected to the isolation of FeOB.
67770Paddy field soil in AnjoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Paddy (Ricefield)
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 66622
  • description: Ferrigenium kumadai gene for 16S ribosomal RNA, partial sequence
  • accession: LC065124
  • length: 1462
  • database: ena
  • NCBI tax ID: 1682490

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ferrigenium kumadai An22GCA_018324385completencbi1682490
66792Ferrigenium kumadai strain An221682490.3completepatric1682490
66792Ferrigenium kumadai An222927562029draftimg1682490

GC content

@refGC-contentmethod
6662261.4high performance liquid chromatography (HPLC)
6777064.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes63.716no
gram-positiveno99.358no
anaerobicno85.493no
aerobicno96.082yes
halophileno97.39no
spore-formingno93.966yes
thermophileno90.818yes
glucose-utilno64.14no
motileyes94.097no
glucose-fermentno86.404no

External links

@ref: 66622

culture collection no.: JCM 30584, NBRC 112974, ATCC TSD-51

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29944111Ferrigenium kumadai gen. nov., sp. nov., a microaerophilic iron-oxidizing bacterium isolated from a paddy field soil.Khalifa A, Nakasuji Y, Saka N, Honjo H, Asakawa S, Watanabe TInt J Syst Evol Microbiol10.1099/ijsem.0.0028822018Autotrophic Processes, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gallionellaceae/*classification/genetics/isolation & purification, Iron/metabolism, Japan, *Oryza, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Genetics34236217Complete Genome Sequence of Ferrigenium kumadai An22, a Microaerophilic Iron-Oxidizing Bacterium Isolated from a Paddy Field Soil.Watanabe T, Khalifa A, Asakawa SMicrobiol Resour Announc10.1128/MRA.00346-212021Phylogeny

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
66622Ashraf Khalifa, Yuta Nakasuji, Norikuni Saka, Hiroki Honjo, Susumu Asakawa, Takeshi WatanabeFerrigenium kumadai gen. nov., sp. nov., a microaerophilic iron-oxidizing bacterium isolated from a paddy field soil10.1099/ijsem.0.002882IJSEM 68: 2587-2592 201829944111
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1