Strain identifier

BacDive ID: 158274

Type strain: No

Species: Thioclava sediminum

Strain Designation: ElOx 9

Strain history: <- L. Bird, Univ. of Southern California, USA; ElOx 9 <- A. Rowe, Univ. of Southern California, USA

NCBI tax ID(s): 1549850 (species)

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General

@ref: 64933

BacDive-ID: 158274

DSM-Number: 103712

keywords: 16S sequence, Bacteria, anaerobe, halotolerant, autotroph, mesophilic, Gram-negative, motile, rod-shaped

description: Thioclava sediminum ElOx 9 is an anaerobe, halotolerant, autotroph bacterium that was isolated from Marine sediments.

NCBI tax id

  • NCBI tax id: 1549850
  • Matching level: species

strain history

  • @ref: 64933
  • history: <- L. Bird, Univ. of Southern California, USA; ElOx 9 <- A. Rowe, Univ. of Southern California, USA

doi: 10.13145/bacdive158274.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Thioclava
  • species: Thioclava sediminum
  • full scientific name: Thioclava sediminum Liu et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Thioclava electrotropha

@ref: 64933

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Thioclava

species: Thioclava sediminum

full scientific name: Thioclava sediminum Liu et al. 2017

strain designation: ElOx 9

type strain: no

Morphology

cell morphology

  • @ref: 65564
  • gram stain: negative
  • cell length: 1-2 µm
  • cell width: 0.3-0.7 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 65564
  • colony color: yellow
  • medium used: rich media

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64933BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
65564rich mediayes

culture temp

@refgrowthtypetemperaturerange
64933positivegrowth30mesophilic
65564positivegrowth10-41
65564positiveoptimum37mesophilic

culture pH

@refabilitytypepHPH range
65564positivegrowth4.5-8.5alkaliphile
65564positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 65564
  • oxygen tolerance: anaerobe

nutrition type

  • @ref: 65564
  • type: autotroph

halophily

@refhalophily levelsaltgrowthtested relationconcentration
65564halotolerantNaClpositivegrowth0-10 %(w/v)
65564NaClpositiveoptimum2 %(w/v)

observation

  • @ref: 65564
  • observation: forms biofilms on mineral or electrode surfaces

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65564167632-oxobutanoate+oxidation
65564309162-oxoglutarate+oxidation
65564286442-oxopentanoate-oxidation
65564620642,3-butanediol-oxidation
65564182404-hydroxy-L-proline-oxidation
65564181014-hydroxyphenylacetic acid-oxidation
6556430089acetate+growth
6556430089acetate+oxidation
6556417128adipate-assimilation
6556415963ribitol-oxidation
6556440585alpha-cyclodextrin+oxidation
6556417925alpha-D-glucose+oxidation
6556417665alpha-D-glucose 6-phosphate-oxidation
65564645522-hydroxybutyrate+oxidation
6556436219alpha-lactose-oxidation
655648295beta-hydroxybutyrate+oxidation
6556473706bromosuccinate+oxidation
6556427689decanoate-assimilation
6556417057cellobiose+oxidation
6556416383cis-aconitate+oxidation
6556416947citrate-oxidation
6556415570D-alanine-oxidation
6556418333D-arabitol+oxidation
6556415824D-fructose+oxidation
6556415895D-galactonic acid lactone-oxidation
6556412936D-galactose+oxidation
6556418024D-galacturonic acid-oxidation
655648391D-gluconate+oxidation
6556417784D-glucosaminic acid-oxidation
6556417634D-glucose+assimilation
6556415748D-glucuronate-oxidation
6556416899D-mannitol-oxidation
6556416899D-mannitol+assimilation
6556416024D-mannose-oxidation
6556416024D-mannose+assimilation
6556427605D-psicose+oxidation
6556433801D-saccharate-oxidation
6556416523D-serine-oxidation
6556417924D-sorbitol-oxidation
6556423652dextrin+oxidation
6556418276dihydrogen+oxidation
6556417126DL-carnitine-oxidation
6556424996lactate+oxidation
6556433403elemental sulfur+oxidation
6556417113erythritol+oxidation
6556416000ethanolamine-oxidation
6556415740formate-growth
6556415740formate-oxidation
6556416865gamma-aminobutyric acid-oxidation
65564167244-hydroxybutyrate+oxidation
6556428066gentiobiose-oxidation
6556417234glucose-fermentation
6556417234glucose+growth
6556429042glucose 1-phosphate-oxidation
6556432323glucuronamide-oxidation
6556417754glycerol+oxidation
6556414336glycerol 1-phosphate-oxidation
6556428087glycogen+oxidation
6556473804glycyl L-aspartic acid-oxidation
6556417596inosine-oxidation
6556417268myo-inositol-oxidation
6556417240itaconate-oxidation
6556421217L-alaninamide+oxidation
6556416977L-alanine+oxidation
6556473786L-alanylglycine+oxidation
6556430849L-arabinose+assimilation
6556417196L-asparagine-oxidation
6556429991L-aspartate-oxidation
6556428120L-fructose-oxidation
6556429985L-glutamate-oxidation
6556415971L-histidine+oxidation
6556415603L-leucine-oxidation
6556415729L-ornithine-oxidation
6556417295L-phenylalanine-oxidation
6556417203L-proline+oxidation
6556418183L-pyroglutamic acid-oxidation
6556462345L-rhamnose-oxidation
6556417115L-serine-oxidation
6556416857L-threonine-oxidation
655646359lactulose-oxidation
6556425115malate-assimilation
6556415792malonate-oxidation
6556417306maltose+assimilation
6556417306maltose+oxidation
6556428053melibiose-oxidation
65564320055methyl beta-D-glucopyranoside+oxidation
6556451850methyl pyruvate+oxidation
6556475146monomethyl succinate+oxidation
65564506227N-acetylglucosamine-assimilation
65564506227N-acetylglucosamine-oxidation
6556473784glycyl-l-glutamate-oxidation
6556417632nitrate+electron acceptor
6556417632nitrate+reduction
6556418401phenylacetate-assimilation
6556450048phenylethylamine-oxidation
6556432032potassium gluconate+assimilation
6556417272propionate+oxidation
6556417148putrescine-oxidation
6556426490quinate-oxidation
6556416634raffinose+oxidation
6556441865sebacic acid-oxidation
6556453258sodium citrate-assimilation
65564143136succinamate+oxidation
6556430031succinate+oxidation
6556417992sucrose+oxidation
6556416094thiosulfate+oxidation
6556417748thymidine+oxidation
6556427082trehalose+oxidation
6556432528turanose+oxidation
6556453423tween 40-oxidation
6556453426tween 80-oxidation
6556416704uridine+oxidation
6556427248urocanic acid-oxidation
6556417151xylitol-oxidation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6556428077rifampicinyesyes5 µg/mL
6556417833gentamicinyesyes10 µg/mL
6556428971ampicillinyesyes10 µg/mL
655646104kanamycinyesyes30 µg/mL
6556427902tetracyclineyesyes30 µg/mL
6556417698chloramphenicolyesyes30 µg/mL
655649215spectinomycinyesyes50 µg/mL
6556417076streptomycinyesyes10 µg/mL

enzymes

@refvalueactivityec
65564catalase+1.11.1.6
65564cytochrome oxidase+1.9.3.1
65564alkaline phosphatase+3.1.3.1
65564esterase (C 4)+
65564esterase Lipase (C 8)+
65564leucine arylamidase+3.4.11.1
65564valine arylamidase+
65564acid phosphatase+3.1.3.2
65564naphthol-AS-BI-phosphohydrolase+
65564alpha-galactosidase+3.2.1.22
65564alpha-glucosidase+3.2.1.20
65564lipase (C 14)-
65564cystine arylamidase-3.4.11.3
65564trypsin-3.4.21.4
65564alpha-chymotrypsin-3.4.21.1
65564beta-galactosidase-3.2.1.23
65564beta-glucuronidase-3.2.1.31
65564beta-glucosidase-3.2.1.21
65564N-acetyl-beta-glucosaminidase-3.2.1.52
65564alpha-mannosidase-3.2.1.24
65564alpha-fucosidase-3.2.1.51
65564arginine dihydrolase+3.5.3.6
65564urease+3.5.1.5
65564beta-glucosidase+3.2.1.21
65564beta-galactosidase+3.2.1.23
65564gelatinase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureisolation procedure
64933Marine sedimentsCalifornia, LA county, Catalina Harbor (33° 25' 13.8'' N, 118° 19' 25.2'' W)USAUSANorth America33.4205-118.324
65564marine sedimentCatalina Harbor, CaliforniaUSAUSANorth America33.4205-118.324Sediment microcosm and artificial anoxic salt water mediumIndium tin oxide plated glass electrodes were placed in the sediment microcosm and maintained at poised electron donating potentials. Sediemnt-enriched electrodes were placed into electrochemical reactors with an artificial anoxic salt water medium.

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_1484.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_849;97_991;98_1170;99_1484&stattab=map
  • Last taxonomy: Thioclava
  • 16S sequence: MG208121
  • Sequence Identity:
  • Total samples: 2098
  • soil counts: 226
  • aquatic counts: 1428
  • animal counts: 413
  • plant counts: 31

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
64933Thioclava sp. ElOx 9 16S ribosomal RNA gene, partial sequenceKM088033802ena1549850
64933Thioclava sp. ElOx9 strain ELOx9 16S ribosomal RNA gene, partial sequenceMG2081211473ena1549850

GC content

  • @ref: 65564
  • GC-content: 63.8
  • method: genome sequence analysis

External links

@ref: 64933

culture collection no.: DSM 103712

straininfo link

  • @ref: 111092
  • straininfo: 399037

literature

  • topic: Phylogeny
  • Pubmed-ID: 29570444
  • title: Thioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments.
  • authors: Chang R, Bird L, Barr C, Osburn M, Wilbanks E, Nealson K, Rowe A
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002723
  • year: 2018
  • mesh: Autotrophic Processes, Bacterial Typing Techniques, Base Composition, California, DNA, Bacterial/genetics, Electrodes, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Salinity, Seawater/*microbiology, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
64933Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103712Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103712)
65564Rachel Chang, Lina Bird, Casey Barr, Magdalena Osburn, Elizabeth Wilbanks, Kenneth Nealson and Annette RoweThioclava electrotropha sp. nov., a versatile electrode and sulfur-oxidizing bacterium from marine sediments10.1099/ijsem.0.002723IJSEM 68: 1652-1658 201829570444
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/
111092Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399037.1