Strain identifier

BacDive ID: 140898

Type strain: Yes

Species: Nitrincola alkalisediminis

Strain Designation: MEB087

Strain history: A. A. Joshi MEB087.

NCBI tax ID(s): 1366656 (species)

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General

@ref: 43735

BacDive-ID: 140898

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

description: Nitrincola alkalisediminis MEB087 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from A sediment sample collected from the alkaline Lonar Lake.

NCBI tax id

  • NCBI tax id: 1366656
  • Matching level: species

strain history

  • @ref: 67770
  • history: A. A. Joshi MEB087.

doi: 10.13145/bacdive140898.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Oceanospirillaceae
  • genus: Nitrincola
  • species: Nitrincola alkalisediminis
  • full scientific name: Nitrincola alkalisediminis Joshi et al. 2016

@ref: 43735

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Oceanospirillaceae

genus: Nitrincola

species: Nitrincola alkalisediminis

strain designation: MEB087

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43735negative1.4-2.2 µm0.7-1.17 µmrod-shapedno
69480yes97.982
69480negative99.999

colony morphology

  • @ref: 43735
  • colony size: 2-5 mm
  • colony color: Cream
  • colony shape: circular
  • incubation period: 2 days
  • medium used: Nutrient agar

Culture and growth conditions

culture medium

  • @ref: 43735
  • name: Nutrient agar (NA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43735positiveoptimum37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
43735positivegrowth7.5-11alkaliphile
43735positiveoptimum9.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43735
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.919

halophily

@refsaltgrowthtested relationconcentration
43735NaClpositivegrowth0.6 M
43735NaClpositiveoptimum0.4 M

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4373530089acetate-carbon source
4373517128adipate-carbon source
4373515963ribitol-carbon source
4373527689decanoate-carbon source
4373517057cellobiose-carbon source
4373523399coumarate-carbon source
4373517108D-arabinose-carbon source
4373515824D-fructose-carbon source
4373512936D-galactose-carbon source
4373516024D-mannose-carbon source
4373516988D-ribose-carbon source
4373565327D-xylose-carbon source
4373524996lactate-carbon source
4373516813galactitol-carbon source
4373516236ethanol-carbon source
4373529806fumarate-carbon source
4373524297glucuronate-carbon source
4373517754glycerol-carbon source
4373515428glycine-carbon source
43735606565hippurate-carbon source
4373516977L-alanine-carbon source
4373516467L-arginine-carbon source
4373517196L-asparagine-carbon source
4373529991L-aspartate-carbon source
4373529985L-glutamate-carbon source
4373518050L-glutamine-carbon source
4373517191L-isoleucine-carbon source
4373515603L-leucine-carbon source
4373516643L-methionine-carbon source
4373515729L-ornithine-carbon source
4373517295L-phenylalanine-carbon source
4373562345L-rhamnose-carbon source
4373517115L-serine-carbon source
4373516857L-threonine-carbon source
4373516828L-tryptophan-carbon source
4373517716lactose-carbon source
4373525115malate-carbon source
4373517306maltose-carbon source
4373529864mannitol-carbon source
43735506227N-acetylglucosamine-carbon source
4373518401phenylacetate-carbon source
4373532032potassium gluconate-carbon source
4373528831propanol-carbon source
4373515611sarcosine-carbon source
4373530911sorbitol-carbon source
4373530031succinate-carbon source
4373530089acetate-energy source
4373517128adipate-energy source
4373515963ribitol-energy source
4373527689decanoate-energy source
4373517057cellobiose-energy source
4373523399coumarate-energy source
4373517108D-arabinose-energy source
4373515824D-fructose-energy source
4373512936D-galactose-energy source
4373516024D-mannose-energy source
4373516988D-ribose-energy source
4373565327D-xylose-energy source
4373524996lactate-energy source
4373516813galactitol-energy source
4373516236ethanol-energy source
4373529806fumarate-energy source
4373524297glucuronate-energy source
4373517754glycerol-energy source
4373515428glycine-energy source
43735606565hippurate-energy source
4373516977L-alanine-energy source
4373516467L-arginine-energy source
4373517196L-asparagine-energy source
4373529991L-aspartate-energy source
4373529985L-glutamate-energy source
4373518050L-glutamine-energy source
4373517191L-isoleucine-energy source
4373515603L-leucine-energy source
4373516643L-methionine-energy source
4373515729L-ornithine-energy source
4373517295L-phenylalanine-energy source
4373562345L-rhamnose-energy source
4373517115L-serine-energy source
4373516857L-threonine-energy source
4373516828L-tryptophan-energy source
4373517716lactose-energy source
4373525115malate-energy source
4373517306maltose-energy source
4373529864mannitol-energy source
43735506227N-acetylglucosamine-energy source
4373518401phenylacetate-energy source
4373532032potassium gluconate-energy source
4373528831propanol-energy source
4373515611sarcosine-energy source
4373530911sorbitol-energy source
4373530031succinate-energy source
43735casein-hydrolysis
4373516991dna-hydrolysis
437355291gelatin-hydrolysis
4373528017starch-hydrolysis
4373516199urea-hydrolysis
4373517634D-glucose+carbon source
4373533801D-saccharate+carbon source
4373525115malate+carbon source
4373515361pyruvate+carbon source
4373553258sodium citrate+carbon source
4373517992sucrose+carbon source
4373517234glucose+fermentation
4373517632nitrate+reduction
4373516301nitrite+reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4373548923erythromycinyesyes15 µg (disc)
437358309polymyxin byesyes35 µg (disc)
4373517833gentamicinyesyes5 µg (disc)
4373517076streptomycinyesyes10 µg (disc)
4373528077rifampicinyesyes2 µg (disc)
4373527902tetracyclineyesyes30 µg (disc)
43735100147nalidixic acidyesyes30 µg (disc)
437357507neomycinyesyes30 µg (disc)
4373517698chloramphenicolyesyes30 µg (disc)
4373517334penicillinyesyes10 µg (disc)
4373528669bacitracinyesyes10 Unit (disc)
437353393carbenicillinyesyes100 µg (disc)
4373528971ampicillinyesyes25 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4373515688acetoinno
4373516136hydrogen sulfideno
4373535581indoleno

metabolite tests

  • @ref: 43735
  • Chebi-ID: 17234
  • metabolite: glucose
  • methylred-test: +

enzymes

@refvalueactivityec
43735cytochrome oxidase+1.9.3.1
43735catalase+1.11.1.6
43735lysine decarboxylase-4.1.1.18
43735arginine dihydrolase-3.5.3.6
43735ornithine decarboxylase-4.1.1.17

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
43735A sediment sample collected from the alkaline Lonar LakeLonar Lake, IndiaIndiaINDAsia2010-10
67770Sediment from the alkaline Lonar Lake in MaharashtraIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Condition#Alkaline
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_4079.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_240;96_2070;97_2495;98_3087;99_4079&stattab=map
  • Last taxonomy: Nitrincola
  • 16S sequence: KC822363
  • Sequence Identity:
  • Total samples: 90
  • soil counts: 10
  • aquatic counts: 54
  • animal counts: 25
  • plant counts: 1

Sequence information

16S sequences

  • @ref: 43735
  • description: 16S rRNA gene sequence
  • accession: KC822363
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nitrincola alkalisediminis JCM 19317GCA_009821115scaffoldncbi1366656
66792Nitrincola alkalisediminis strain MEB0871366656.3wgspatric1366656
66792Nitrincola alkalisediminis JCM 193172890467569draftimg1366656

GC content

  • @ref: 67770
  • GC-content: 49.3
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.657yes
flagellatedyes95.226no
gram-positiveno98.727yes
anaerobicno98.312yes
aerobicyes83.136no
halophileyes66.496no
spore-formingno93.614no
glucose-utilyes83.566yes
thermophileno98.797yes
glucose-fermentno76.255yes

External links

@ref: 43735

culture collection no.: KCTC 42948, JCM 19317

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26705145Nitrincola alkalisediminis sp. nov., an alkaliphilic bacterium isolated from an alkaline lake.Joshi A, Thite S, Kulkarni G, Dhotre D, Joseph N, Venkata Ramana V, Polkade A, Shouche YInt J Syst Evol Microbiol10.1099/ijsem.0.0008682015Alkalies, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Lakes/*microbiology, Nucleic Acid Hybridization, Oceanospirillaceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny30431420Nitrincola tibetensis sp. nov., isolated from Lake XuguoCo on the Tibetan Plateau.Phurbu D, Pema Y, Ma C, Lu H, Li H, Tian Y, Xing PInt J Syst Evol Microbiol10.1099/ijsem.0.0031112018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Nucleic Acid Hybridization, Oceanospirillaceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Ubiquinone/chemistryTranscriptome

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
43735Amaraja Joshi, Sonia Thite, Girish Kulkarni, Dhiraj Dhotre, Neetha Joseph, Venkata Ramana V., Ashish Polkade, Yogesh ShoucheNitrincola alkalisediminis sp. nov., an alkaliphilic bacterium isolated from an alkaline lake10.1099/ijsem.0.000868IJSEM 66: 1254-1259 201626705145
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/
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