Strain identifier

BacDive ID: 158570

Type strain: Yes

Species: Cohnella algarum

Strain Designation: Pch-40

Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; Pch-40.

NCBI tax ID(s): 2044859 (species)

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General

@ref: 65270

BacDive-ID: 158570

keywords: genome sequence, 16S sequence, Bacteria, facultative aerobe, spore-forming, Gram-positive, motile, rod-shaped, colony-forming

description: Cohnella algarum Pch-40 is a facultative aerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from freshwater green alga P. chromatophora.

NCBI tax id

  • NCBI tax id: 2044859
  • Matching level: species

strain history

  • @ref: 67770
  • history: C. O. Jeon; Chung-Ang Univ., South Korea; Pch-40.

doi: 10.13145/bacdive158570.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Cohnella
  • species: Cohnella algarum
  • full scientific name: Cohnella algarum Lee and Jeon 2017

@ref: 65270

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Paenibacillaceae

genus: Cohnella

species: Cohnella algarum

strain designation: Pch-40

type strain: yes

Morphology

cell morphology

  • @ref: 65270
  • gram stain: positive
  • cell length: 2.5-2.7 µm
  • cell width: 0.9-1 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: monotrichous, polar

colony morphology

  • @ref: 65270
  • colony size: 1-1.5 mm
  • colony color: creamy white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A

Culture and growth conditions

culture medium

@refnamegrowth
65270Reasoner's 2A agar (R2A)yes
65270Nutrient agar (NA)yes
65270tryptic soy agaryes

culture temp

@refgrowthtypetemperaturerange
65270positivegrowth20-50
65270positivegrowth37-40
67770positivegrowth40thermophilic

culture pH

@refabilitytypepHPH range
65270positivegrowth5-11alkaliphile
65270positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 65270
  • oxygen tolerance: facultative aerobe

spore formation

  • @ref: 65270
  • spore description: Subterminal ellipsoidal endospores are observed in swollen sporangia
  • type of spore: endospore
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
65270NaClpositivegrowth0-4 %(w/v)
65270NaClpositiveoptimum0 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65270645522-hydroxybutyrate-oxidation
65270167632-oxobutanoate-oxidation
65270309162-oxoglutarate+oxidation
65270286442-oxopentanoate-oxidation
65270620642,3-butanediol+oxidation
65270370543-hydroxybutyrate+oxidation
65270182404-hydroxy-L-proline+oxidation
65270167244-hydroxybutyrate+oxidation
65270181014-hydroxyphenylacetic acid+oxidation
652703557154-nitrophenyl beta-D-galactopyranoside+assimilation
6527030089acetate+oxidation
6527017128adipate-assimilation
6527015963ribitol+oxidation
6527040585alpha-cyclodextrin+oxidation
6527017925alpha-D-glucose+oxidation
6527036219alpha-lactose+oxidation
6527073706bromosuccinate+oxidation
6527027689decanoate-assimilation
65270casein-hydrolysis
6527016383cis-aconitate+oxidation
6527016947citrate+oxidation
6527015570D-alanine+oxidation
6527018333D-arabitol+oxidation
6527017057cellobiose+oxidation
6527015824D-fructose+oxidation
6527015895D-galactonic acid lactone+oxidation
6527012936D-galactose+oxidation
6527018024D-galacturonic acid+oxidation
6527030612D-glucarate+oxidation
652708391D-gluconate+oxidation
6527017784D-glucosaminic acid+oxidation
6527017634D-glucose+assimilation
6527014314D-glucose 6-phosphate+oxidation
6527015748D-glucuronate+oxidation
6527016899D-mannitol-assimilation
6527016899D-mannitol+oxidation
6527016024D-mannose+assimilation
6527016024D-mannose+oxidation
6527027605D-psicose+oxidation
6527016523D-serine+oxidation
6527017924D-sorbitol+oxidation
6527023652dextrin+oxidation
6527017126DL-carnitine+oxidation
6527024996lactate+oxidation
6527017113erythritol-oxidation
652704853esculin+hydrolysis
65270esculin ferric citrate+assimilation
6527016000ethanolamine+oxidation
6527015740formate+oxidation
6527016865gamma-aminobutyric acid+oxidation
652705291gelatin-assimilation
6527028066gentiobiose+oxidation
6527029042glucose 1-phosphate+oxidation
6527032323glucuronamide-oxidation
6527017754glycerol+oxidation
6527014336glycerol 1-phosphate+oxidation
6527028087glycogen+oxidation
6527073804glycyl L-aspartic acid-oxidation
6527017596inosine+oxidation
6527017240itaconate-oxidation
6527021217L-alaninamide-oxidation
6527016977L-alanine+oxidation
6527073786L-alanylglycine+oxidation
6527030849L-arabinose+assimilation
6527030849L-arabinose+oxidation
6527016467L-arginine-assimilation
6527017196L-asparagine+oxidation
6527029991L-aspartate+oxidation
6527018287L-fucose+oxidation
6527029985L-glutamate+oxidation
6527015971L-histidine+oxidation
6527015603L-leucine+oxidation
6527015729L-ornithine+oxidation
6527017295L-phenylalanine-oxidation
6527017203L-proline+oxidation
6527018183L-pyroglutamic acid+oxidation
6527062345L-rhamnose+oxidation
6527017115L-serine+oxidation
6527016857L-threonine-oxidation
6527016828L-tryptophan-assimilation
652706359lactulose+oxidation
6527025115malate-assimilation
6527015792malonate+oxidation
6527017306maltose+assimilation
6527017306maltose+oxidation
6527028053melibiose+oxidation
65270320055methyl beta-D-glucopyranoside+oxidation
6527051850methyl pyruvate+oxidation
6527075146monomethyl succinate+oxidation
6527017268myo-inositol+oxidation
6527028037N-acetylgalactosamine+oxidation
65270506227N-acetylglucosamine-assimilation
65270506227N-acetylglucosamine+oxidation
6527073784glycyl-l-glutamate-oxidation
6527017632nitrate-reduction
6527018401phenylacetate-assimilation
6527050048phenylethylamine+oxidation
6527032032potassium gluconate-assimilation
6527017272propionate+oxidation
6527017148putrescine+oxidation
6527026490quinate+oxidation
6527016634raffinose+oxidation
6527041865sebacic acid+oxidation
6527053258sodium citrate-assimilation
6527028017starch+hydrolysis
65270143136succinamate-oxidation
6527030031succinate+oxidation
6527017992sucrose+oxidation
6527017748thymidine+oxidation
6527027082trehalose+oxidation
6527032528turanose+oxidation
6527053424tween 20-hydrolysis
6527053423tween 40+oxidation
6527053426tween 80-hydrolysis
6527053426tween 80+oxidation
6527018186tyrosine-hydrolysis
6527016199urea+assimilation
6527016704uridine+oxidation
6527027248urocanic acid+oxidation
6527017151xylitol-oxidation

enzymes

@refvalueactivityec
65270cytochrome oxidase+1.9.3.1
65270catalase+1.11.1.6
65270alkaline phosphatase+3.1.3.1
65270esterase (C 4)+
65270esterase Lipase (C 8)+
65270lipase (C 14)+
65270acid phosphatase+3.1.3.2
65270naphthol-AS-BI-phosphohydrolase+
652706-phospho-beta-galactosidase+3.2.1.85
65270alpha-glucosidase+3.2.1.20
65270leucine arylamidase+3.4.11.1
65270valine arylamidase+
65270alpha-galactosidase+3.2.1.22
65270beta-glucuronidase+3.2.1.31
65270beta-glucosidase+3.2.1.21
65270cystine arylamidase-3.4.11.3
65270alpha-chymotrypsin-3.4.21.1
65270trypsin-3.4.21.4
65270N-acetyl-beta-glucosaminidase-3.2.1.52
65270alpha-mannosidase-3.2.1.24
65270alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65270C16:06.5
    65270C14:0 iso2.4
    65270C15:0 iso3.6
    65270C16:0 iso44.5
    65270C17:0 iso1.1
    65270C15:0 anteiso30.8
    65270C17:0 anteiso6
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A broth
  • incubation temperature: 40
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedurehost species
65270freshwater green alga P. chromatophorawater reservoir located in Chungcheongnam-doRepublic of KoreaKORAsia36.561126.762DY-V medium20 mg MES, 5 mg MgSO4 x 7H2O, 0.3 mg KCl, 0.27 mg NH4Cl, 2 mg NaNO3 , 0.22 mg b-Na 2 glycerophosphate x 5H2O, 0.08 mg H3BO3, 0.8 mg Na2EDTA x 2H2O, 1.4 mg Na2SiO3 x 9H2O, 0.1 mg FeCl3 x 6H2O, 7.5 mg CaCl2 x 2H2O, 0.05 µg vitamin B12 , 0.05 µg biotin, 10 µg thiamine hydrochloride, 20 µg MnCl2 x 4H2O, 4 µg ZnSO4 x 7H2O, 0.8 µg CoCl2 x 6H2O, 2 µg Na2MoO4 x 2H2O, 0.2 µg Na3VO4, 0.2 µg H2SeO3, per litre, pH 6.84 weeks25cultivated at 25°C for 4 weeks in DY-V medium under alternating light and dark conditions. After the cells of P. chromatophora were homogenized using a homogenizer for 1 min, the samples were serially diluted in fresh DY-V medium. The aliquots of each serial dilution were spread onto R2A agar (BD) and incubated aerobically at 25°C for 3 days.
67770Freshwater green alga, Paulinella chromatophora, from a water reservoirChungcheongnam-doRepublic of KoreaKORAsiaPaulinella chromatophora

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Freshwater
#Host#Algae#Green algae

taxonmaps

  • @ref: 69479
  • File name: preview.99_5664.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_2723;97_3347;98_4218;99_5664&stattab=map
  • Last taxonomy: Cohnella
  • 16S sequence: KY864397
  • Sequence Identity:
  • Total samples: 48
  • soil counts: 21
  • aquatic counts: 2
  • animal counts: 19
  • plant counts: 6

Sequence information

16S sequences

  • @ref: 65270
  • description: 16S rRNA gene sequence
  • accession: KY864397
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Cohnella algarum Pch-40
  • accession: GCA_016937515
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 2044859

GC content

@refGC-contentmethod
6527055.6real time PCR (RTD-PCR)
6777055.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes83.143no
gram-positiveyes88.274no
anaerobicno98.775yes
aerobicyes78.921yes
halophileno94.206yes
spore-formingyes94.664yes
thermophileno93.195yes
glucose-utilyes89.553yes
motileyes89.729yes
glucose-fermentno90.376no

External links

@ref: 65270

culture collection no.: KACC 19279, JCM 32033

literature

  • topic: Phylogeny
  • Pubmed-ID: 28984547
  • title: Cohnella algarum sp. nov., isolated from a freshwater green alga Paulinella chromatophora.
  • authors: Lee Y, Jeon CO
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002377
  • year: 2017
  • mesh: Bacillales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chlorophyta/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • 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
65270Yunho Lee, Che Ok JeonCohnella algarum sp. nov., isolated from a freshwater green alga Paulinella chromatophora10.1099/ijsem.0.002377IJSEM 67: 4767-4772 201728984547
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/
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/