Strain identifier

BacDive ID: 140928

Type strain: Yes

Species: Marivivens donghaensis

Strain Designation: AM-4

NCBI tax ID(s): 1699413 (species)

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General

@ref: 43800

BacDive-ID: 140928

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

description: Marivivens donghaensis AM-4 is an aerobe, Gram-negative, pleomorphic-shaped bacterium that forms circular colonies and was isolated from Seawater collected from the East Sea.

NCBI tax id

  • NCBI tax id: 1699413
  • Matching level: species

doi: 10.13145/bacdive140928.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Roseobacteraceae
  • genus: Marivivens
  • species: Marivivens donghaensis
  • full scientific name: Marivivens donghaensis Park et al. 2016

  • synonyms

    • @ref: 20215
    • synonym: Aestuarium zhoushanense

@ref: 43800

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Marivivens

species: Marivivens donghaensis

strain designation: AM-4

type strain: yes

Morphology

cell morphology

  • @ref: 43800
  • gram stain: negative
  • cell length: 0.2-10 µm
  • cell width: 0.2-0.6 µm
  • cell shape: pleomorphic-shaped
  • motility: no

colony morphology

  • @ref: 43800
  • colony size: 1.5-3 mm
  • colony color: Greyish-yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: MA agar

Culture and growth conditions

culture medium

  • @ref: 43800
  • name: Marine agar (MA)
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43800positivegrowth10-40
43800positiveoptimum30-35mesophilic

culture pH

@refabilitytypepH
43800positivegrowth6.5-8
43800positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

  • @ref: 43800
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43800NaClpositivegrowth0-6 %(w/v)
43800NaClpositiveoptimum1-3 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4380016150benzoate-carbon source
4380015740formate-carbon source
4380030849L-arabinose-carbon source
4380029985L-glutamate-carbon source
4380017306maltose-carbon source
4380027082trehalose-carbon source
4380016150benzoate-energy source
4380015740formate-energy source
4380030849L-arabinose-energy source
4380029985L-glutamate-energy source
4380017306maltose-energy source
4380027082trehalose-energy source
43800casein-hydrolysis
438005291gelatin-hydrolysis
4380028017starch-hydrolysis
4380053426tween 80-hydrolysis
4380016199urea-hydrolysis
4380015318xanthine-hydrolysis
4380018420magnesium(2+)-required for growth
4380030089acetate+carbon source
4380017057cellobiose+carbon source
4380015824D-fructose+carbon source
4380012936D-galactose+carbon source
4380017634D-glucose+carbon source
4380016024D-mannose+carbon source
4380065327D-xylose+carbon source
4380015361pyruvate+carbon source
4380017814salicin+carbon source
4380017992sucrose+carbon source
4380030089acetate+energy source
4380017057cellobiose+energy source
4380015824D-fructose+energy source
4380012936D-galactose+energy source
4380017634D-glucose+energy source
4380016024D-mannose+energy source
4380065327D-xylose+energy source
4380015361pyruvate+energy source
4380017814salicin+energy source
4380017992sucrose+energy source
438004853esculin+hydrolysis
4380017368hypoxanthine+hydrolysis
4380017632nitrate+reduction
4380016947citrate+/-carbon source
4380030031succinate+/-carbon source
4380016947citrate+/-energy source
4380030031succinate+/-energy source
4380017895L-tyrosine+/-hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4380028971ampicillinyesyes10 µg (disc)
438003393carbenicillinyesyes100 µg (disc)
438003542cephalothinyesyes30 µg (disc)
4380017698chloramphenicolyesyes100 µg (disc)
438006104kanamycinyesyes30 µg (disc)
438007507neomycinyesyes30 µg (disc)
4380028368novobiocinyesyes5 µg (disc)
4380016869oleandomycinyesyes15 µg (disc)
4380017076streptomycinyesyes50 µg (disc)
4380027902tetracyclineyesyes30 µg (disc)
4380018208penicillin gyesyes20 Unit (disc)
4380017833gentamicinyesyes30 µg (disc)
438006472lincomycinyesyes15 µg (disc)
438008309polymyxin byesyes100 Unit (disc)

enzymes

@refvalueactivityec
43800alkaline phosphatase+3.1.3.1
43800esterase (C 4)+
43800esterase Lipase (C 8)+
43800leucine arylamidase+3.4.11.1
43800acid phosphatase+3.1.3.2
43800lipase (C 14)-
43800valine arylamidase-
43800cystine arylamidase-3.4.11.3
43800trypsin-3.4.21.4
43800alpha-chymotrypsin-3.4.21.1
43800naphthol-AS-BI-phosphohydrolase-
43800alpha-galactosidase-3.2.1.22
43800beta-galactosidase-3.2.1.23
43800beta-glucuronidase-3.2.1.31
43800alpha-glucosidase-3.2.1.20
43800beta-glucosidase-3.2.1.21
43800N-acetyl-beta-glucosaminidase-3.2.1.52
43800alpha-mannosidase-3.2.1.24
43800alpha-fucosidase-3.2.1.51
43800catalase+1.11.1.6
43800cytochrome oxidase+1.9.3.1

fatty acid profile

  • @reffatty acidpercentage
    43800C10:0 3OH6.1
    43800C16:012.7
    43800C16:1ω7c / C16:1ω6c8.8
    43800C18:01.9
    43800C18:1ω7c61.4
    4380011-methyl C18:1ω7c8
  • type of FA analysis: whole cell analysis
  • incubation medium: MA plates
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • cutoff value:
  • @reffatty acidpercentage
    43800C10:0 3OH6.3
    43800C16:012.8
    43800C16:1ω7c / C16:1ω6c8.5
    43800C18:01.9
    43800C18:1ω7c61.4
    4380011-methyl C18:1ω7c8.3
  • type of FA analysis: whole cell analysis
  • incubation medium: MA plates
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 3
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • cutoff value:
  • @reffatty acidpercentage
    43800C10:0 3OH9
    43800C16:014
    43800C16:1ω7c / C16:1ω6c7.8
    43800C18:02
    43800C18:1ω7c56.4
    4380011-methyl C18:1ω7c9.1
  • type of FA analysis: whole cell analysis
  • incubation medium: MA plates
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 5
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890
  • cutoff value:
  • @reffatty acidpercentage
    43800C10:0 3OH10.4
    43800C16:015.7
    43800C16:1ω7c / C16:1ω6c5.9
    43800C18:02
    43800C18:1ω7c55.3
    4380011-methyl C18:1ω7c9.3
  • type of FA analysis: whole cell analysis
  • incubation medium: MA plates
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 7
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.2B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43800
  • sample type: Seawater collected from the East Sea
  • geographic location: East Sea
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_1149.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_672;97_778;98_902;99_1149&stattab=map
  • Last taxonomy: Rhodobacteraceae
  • 16S sequence: KT282004
  • Sequence Identity:
  • Total samples: 18468
  • soil counts: 929
  • aquatic counts: 15058
  • animal counts: 2317
  • plant counts: 164

Sequence information

16S sequences

  • @ref: 43800
  • description: 16S rRNA gene sequence
  • accession: KT282004
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Marivivens donghaensis KCTC 42776
  • accession: GCA_023541015
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1699413

GC content

  • @ref: 43800
  • GC-content: 57.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno93.017no
gram-positiveno98.968no
anaerobicno98.309yes
aerobicyes82.953no
halophileyes59.724no
spore-formingno96.755no
motileno88.03yes
glucose-fermentno87.538no
thermophileno92.801yes
glucose-utilyes81.314yes

External links

@ref: 43800

culture collection no.: KCTC 42776, CECT 8947

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26582231Marivivens donghaensis gen. nov., sp. nov., isolated from seawater.Park S, Kim S, Jung YT, Yoon JHInt J Syst Evol Microbiol10.1099/ijsem.0.0007722015
Phylogeny29388535Marivivens niveibacter sp. nov., isolated from the seawater of tropical mangrove.Hu D, Wang L, Lai Q, Sun F, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0025442018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*chemistry, Sequence Analysis, DNA, Ubiquinone/chemistry, *WetlandsTranscriptome
Phylogeny33835235Marivivens aquimaris sp. nov., isolated from seawater.Kim JA, Lee B, Kang JY, Song JJ, Choi JHArch Microbiol10.1007/s00203-021-02305-72021Fatty Acids/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhodobacteraceae/classification/genetics/metabolism, *Seawater/microbiology, Species SpecificityMetabolism
Phylogeny36367506Aestuarium zhoushanense is a later heterotypic synonym of Marivivens donghaensis, and transfer of Paradonghicola geojensis to the genus Marivivens as Marivivens geojensis comb. nov.Qu L, Li Y, Wang W, Shao Z, Gao Z, Lai QInt J Syst Evol Microbiol10.1099/ijsem.0.0055642022RNA, Ribosomal, 16S/genetics, Phylogeny, DNA, Bacterial/genetics, Bacterial Typing Techniques, Base Composition, Sequence Analysis, DNA, *Fatty Acids/chemistry, Nucleic Acid HybridizationTranscriptome

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
43800Sooyeon Park, Sona Kim, Yong-Taek Jung, Jung-Hoon YoonMarivivens donghaensis gen. nov., sp. nov., isolated from seawater10.1099/ijsem.0.000772IJSEM 66: 666-672 201626582231
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
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/