Name: Ferrigenium kumadai An22
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159721

Type strain:

Species: Ferrigenium kumadai

Strain Designation: An22

Culture col. no.: JCM 30584, NBRC 112974, ATCC TSD-51

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

NCBI tax ID(s): 1682490 (species)

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Nitrosomonadales*
	Family	*Gallionellaceae*
	Genus	*Ferrigenium*
	Species	**Ferrigenium kumadai**
	Full Scientific Name (LPSN)	Ferrigenium kumadai Khalifa et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #66622]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.996

[Ref.: #66622]	Cell length	1.43 µm

[Ref.: #66622]	Cell width	0.29 µm

[Ref.: #66622]	Cell shape	rod-shaped

[Ref.: #66622]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %98.055

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #66622]	growth	12-37 °C
[Ref.: #66622]	optimum	25-30 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #66622]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #66622]			optimum	5.9-6.2
[Ref.: #66622]			growth	5.2-6.8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66622]

Oxygen tolerance

microaerophile

[Ref.: #66622]

Nutrition type

lithotroph

[Ref.: #66622]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.99
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66622]		NaCl		growth	1.46	g/L

[Ref.: #66622]	Observation	growing 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.
[Ref.: #67770]	Observation	quinones: Q-10, Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66622]	acetic acid ChEBI	-	energy source
[Ref.: #66622]	citric acid ChEBI	-	energy source
[Ref.: #66622]	dihydrogen ChEBI	-	energy source
[Ref.: #66622]	ferrous ion ChEBI	+	energy source
[Ref.: #66622]	glucose ChEBI	-	energy source
[Ref.: #66622]	manganous ion ChEBI	-	energy source
[Ref.: #66622]	nitrite ChEBI	-	energy source
[Ref.: #66622]	pyruvate ChEBI	-	energy source
[Ref.: #66622]	sulfide ChEBI	-	energy source
[Ref.: #66622]	thiosulfate ChEBI	-	energy source

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #66622]	Sample type/isolated from	soil sample from a paddy field
[Ref.: #66622]	Sampling date	2010-04-13
[Ref.: #66622]	Geographic location (country and/or sea, region)	Crop Institute, Aichi Agricultural Research Centre
[Ref.: #66622]	Country	Japan
[Ref.: #66622]	Country ISO 3 Code	JPN
[Ref.: #66622]	Continent	Asia
[Ref.: #66622]	Geographic location	34.9725°/137.0760°
[Ref.: #66622]	Enrichment culture duration	3-4 weeks
[Ref.: #66622]	Enrichment culture temperature	25 ̊C
[Ref.: #66622]	Isolation/enrichment procedure	Micro-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.

[Ref.: #67770]	Sample type/isolated from	Paddy field soil in Anjo
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66622]	Ferrigenium kumadai gene for 16S ribosomal RNA, partial sequence	LC065124	1462	ENA	1682490 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ferrigenium kumadai An22	GCA_018324385	complete	GenBank	1682490 tax ID	*
[Ref.: #66792]	Ferrigenium kumadai strain An22	1682490.3	complete	PATRIC	1682490 tax ID	*
[Ref.: #66792]	Ferrigenium kumadai An22	2927562029	draft	JGI IMG/M	1682490 tax ID	*

[Ref.: #66622]	GC-content	61.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	64.1 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Ferrigenium kumadai An22 NCBI: GCA_018324385.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ferrigenium kumadai An22 NCBI: GCA_018324385.1
[Ref.: #69480]	flagellated	yes	63.716	no
[Ref.: #69480]	gram-positive	no	99.358	no
[Ref.: #69480]	anaerobic	no	85.493	no
[Ref.: #69480]	aerobic	no	96.082	yes
[Ref.: #69480]	halophile	no	97.39	no
[Ref.: #69480]	spore-forming	no	93.966	yes
[Ref.: #69480]	thermophile	no	90.818	yes
[Ref.: #69480]	glucose-util	no	64.14	no
[Ref.: #69480]	motile	yes	94.097	no
[Ref.: #69480]	glucose-ferment	no	86.404	no

Availability in culture collections External links

[Ref.: #66622]

Culture collection no.

JCM 30584, NBRC 112974, ATCC TSD-51

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete Genome Sequence of Ferrigenium kumadai An22, a Microaerophilic Iron-Oxidizing Bacterium Isolated from a Paddy Field Soil.	Watanabe T, Khalifa A, Asakawa S	Microbiol Resour Announc	10.1128/MRA.00346-21	2021	*
Phylogeny	Ferrigenium 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 T	Int J Syst Evol Microbiol	10.1099/ijsem.0.002882	2018	*

References

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#66622

Ashraf Khalifa, Yuta Nakasuji, Norikuni Saka, Hiroki Honjo, Susumu Asakawa, Takeshi Watanabe: Ferrigenium kumadai gen. nov., sp. nov., a microaerophilic iron-oxidizing bacterium isolated from a paddy field soil. IJSEM 68: 2587 - 2592 2018 ( DOI 10.1099/ijsem.0.002882 , PubMed 29944111 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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