Strain identifier

BacDive ID: 158800

Type strain: Yes

Species: Halomonas endophytica

Strain Designation: MC28

Strain history: <- Can Chen, Zhejiang Univ.

NCBI tax ID(s): 2033802 (species)

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General

@ref: 65561

BacDive-ID: 158800

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

description: Halomonas endophytica MC28 is an aerobe, chemoorganotroph, Gram-negative bacterium that forms circular colonies and was isolated from From storage liquid in the stems of Populus euphratica in xinjiang.

NCBI tax id

  • NCBI tax id: 2033802
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Can Chen, Zhejiang Univ.

doi: 10.13145/bacdive158800.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Oceanospirillales
  • family: Halomonadaceae
  • genus: Halomonas
  • species: Halomonas endophytica
  • full scientific name: Halomonas endophytica Chen et al. 2018

  • synonyms

    • @ref: 20215
    • synonym: Billgrantia endophytica

@ref: 65561

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Oceanospirillales

family: Halomonadaceae

genus: Halomonas

species: Halomonas endophytica

strain designation: MC28

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65561negative1.0-1.5 µm0.5-0.8 µmrod-shapedyes
69480yes97.256
69480negative99.991

colony morphology

  • @ref: 65561
  • colony size: 1-2 mm
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: MA

pigmentation

  • @ref: 65561
  • production: no
  • name: flexirubin-type

Culture and growth conditions

culture medium

  • @ref: 65561
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65561positivegrowth10-45
65561positiveoptimum40thermophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
65561positivegrowth6.0-9.0alkaliphile
65561positiveoptimum8.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
65561aerobe
67771aerobe

nutrition type

  • @ref: 65561
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
69480no99.95
69481no97

halophily

@refsaltgrowthtested relationconcentrationhalophily level
65561NaClpositivegrowth0.5-6.0 %(w/v)
65561NaClpositiveoptimum3 %(w/v)halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6556162968cellulose-hydrolysis
6556185146carboxymethylcellulose-hydrolysis
65561casein-hydrolysis
6556116947citrate+carbon source
6556116947citrate+energy source
6556117108D-arabinose+builds acid from
6556118333D-arabitol+builds acid from
6556115824D-fructose+carbon source
6556115824D-fructose+energy source
6556128847D-fucose-builds acid from
6556112936D-galactose+carbon source
6556112936D-galactose+energy source
6556117634D-glucose+carbon source
6556117634D-glucose+energy source
6556116899D-mannitol+carbon source
6556116899D-mannitol+energy source
6556116024D-mannose+builds acid from
6556116024D-mannose+carbon source
6556116024D-mannose+energy source
6556116988D-ribose+carbon source
6556116988D-ribose+energy source
6556117924D-sorbitol+carbon source
6556117924D-sorbitol+energy source
6556116443D-tagatose+builds acid from
6556116443D-tagatose+carbon source
6556116443D-tagatose+energy source
6556165327D-xylose+builds acid from
6556165327D-xylose+carbon source
6556165327D-xylose+energy source
655615291gelatin-hydrolysis
6556117234glucose-fermentation
6556117234glucose+fermentation
6556130849L-arabinose-builds acid from
6556130849L-arabinose+carbon source
6556130849L-arabinose+energy source
6556117266L-sorbose+builds acid from
6556117266L-sorbose+carbon source
6556117266L-sorbose+energy source
6556117895L-tyrosine-hydrolysis
6556117306maltose-builds acid from
6556117306maltose+carbon source
6556117306maltose+energy source
6556117632nitrate+hydrolysis
6556117632nitrate+reduction
6556184997sodium gluconate+carbon source
6556184997sodium gluconate+energy source
6556128017starch-hydrolysis
6556130031succinate+carbon source
6556130031succinate+energy source
6556117992sucrose-builds acid from
6556117992sucrose+carbon source
6556117992sucrose+energy source
6556127082trehalose-builds acid from
6556127082trehalose+carbon source
6556127082trehalose+energy source
6556132528turanose-builds acid from
6556153424tween 20+hydrolysis
6556153423tween 40+hydrolysis
6556153425tween 60+hydrolysis
6556153426tween 80+hydrolysis
6556118186tyrosine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6556115688acetoinno
6556116136hydrogen sulfideyes

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
6556117234glucose-
6556115688acetoin-

enzymes

@refvalueactivityec
65561catalase+1.11.1.6
65561cytochrome oxidase+1.9.3.1
65561alkaline phosphatase+3.1.3.1
65561esterase (C 4)+
65561esterase Lipase (C 8)+
65561lipase (C 14)+
65561leucine arylamidase+3.4.11.1
65561valine arylamidase+
65561cystine arylamidase+3.4.11.3
65561acid phosphatase+3.1.3.2
65561naphthol-AS-BI-phosphohydrolase+
65561alpha-glucosidase+3.2.1.20
65561urease-3.5.1.5
65561trypsin+3.4.21.4

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
67771From storage liquid in the stems of Populus euphratica in xinjiangChinaCHNAsia
65561liquid samples from stems of Populus euphraticaChinaCHNAsia2016Ebinur Lake Wetland Nature Reserve, Xinjiang Province44.416783.6833MA5 days28

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Plant#Stem (Branch)
#Host#Plants#Tree
#Host Body Product#Plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_30704.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_48;96_15028;97_18350;98_22842;99_30704&stattab=map
  • Last taxonomy: Halomonas
  • 16S sequence: MF850257
  • Sequence Identity:
  • Total samples: 78
  • soil counts: 11
  • aquatic counts: 17
  • animal counts: 46
  • plant counts: 4

Sequence information

16S sequences

  • @ref: 65561
  • description: 16S rRNA gene sequence
  • accession: MF850257
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halomonas endophytica MC28GCA_002879615scaffoldncbi2033802
66792Halomonas endophytica MC282859108715draftimg2033802

GC content

  • @ref: 65561
  • GC-content: 64.1
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
flagellatedyes60.607no
gram-positiveno98.497yes
anaerobicno98.301no
aerobicyes85.183yes
halophileyes83.715no
spore-formingno93.917no
glucose-utilyes87.51no
thermophileno98.54no
motileyes89.707no
glucose-fermentno77.243no

External links

@ref: 65561

culture collection no.: KCTC 52999, MCCC 1K03343

literature

  • topic: Phylogeny
  • Pubmed-ID: 29561252
  • title: Halomonas endophytica sp. nov., isolated from liquid in the stems of Populus euphratica.
  • authors: Chen C, Anwar N, Wu C, Fu G, Wang R, Zhang C, Wu Y, Sun C, Wu M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002585
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Halomonas/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Stems/microbiology, Populus/*microbiology, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • 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
65561Can Chen, Nusratgul Anwar, Chen Wu, Geyi Fu, Ruijun Wang, Choangya Zhang, Yuehong Wu, Cong Sun and Min WuHalomonas endophytica sp. nov., isolated from liquid in the stems of Populus euphratica10.1099/ijsem.0.002585IJSEM 68: 1633-1638 201829561252
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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