Strain identifier

BacDive ID: 7350

Type strain: Yes

Species: Leucobacter aridicollis

Strain Designation: L-9, L9

Strain history: CIP <- 2004, P. Morais, Coimbra, Portugal: strain L9

NCBI tax ID(s): 283878 (species)

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General

@ref: 6937

BacDive-ID: 7350

DSM-Number: 17380

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive

description: Leucobacter aridicollis L-9 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from Activated sludge.

NCBI tax id

  • NCBI tax id: 283878
  • Matching level: species

strain history

@refhistory
6937<- CIP <- P. Morais, strain L9
339542004, P. Morais, Coimbra, Portugal: strain L9
67770LMG 22507 <-- P. V. Morais L-9 <-- R. Francisco.
67772Francisco, R. University of Coimbra
116495CIP <- 2004, P. Morais, Coimbra, Portugal: strain L9

doi: 10.13145/bacdive7350.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Leucobacter
  • species: Leucobacter aridicollis
  • full scientific name: Leucobacter aridicollis Morais et al. 2005

@ref: 6937

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Leucobacter

species: Leucobacter aridicollis

full scientific name: Leucobacter aridicollis Morais et al. 2005

strain designation: L-9, L9

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
116495positiverod-shapedno

colony morphology

  • @ref: 116495

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6937TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
33954MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116495CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6937positivegrowth28mesophilic
33954positivegrowth30mesophilic
67770positivegrowth28mesophilic
67772positiveminimum20psychrophilic
67772positiveoptimum28mesophilic
67772positivemaximum37mesophilic
116495positivegrowth10-37
116495nogrowth41thermophilic
116495nogrowth45thermophilic

culture pH

@refabilitytypepH
67772positivemaximum8.0
67772positiveminimum7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 116495
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no100

halophily

@refsaltgrowthtested relationconcentration
116495NaClpositivegrowth0-6 %
116495NaClnogrowth8 %
116495NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-11

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68368nitrate-reduction17632
68368melibiose-fermentation28053
68368sucrose-fermentation17992
68368L-rhamnose-fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol-fermentation17268
68368D-glucose-fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate-assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
116495D-arabinose-degradation17108
116495D-fructose-degradation15824
116495D-glucose-degradation17634
116495D-mannose-degradation16024
116495D-xylose-degradation65327
116495cellobiose-degradation17057
116495lactose-degradation17716
116495maltose-degradation17306
116495salicin-degradation17814
116495sucrose-degradation17992
116495citrate-carbon source16947
116495esculin-hydrolysis4853
116495hippurate+hydrolysis606565
116495nitrate-reduction17632
116495nitrite-reduction16301
116495nitrate-respiration17632
68376esculin-hydrolysis4853
68376D-arabitol-builds acid from18333
68376D-xylose-builds acid from65327
68376L-rhamnose-builds acid from62345
68376methyl alpha-D-glucopyranoside-builds acid from320061
68376D-ribose-builds acid from16988
68376glucose 1-phosphate-builds acid from29042
68376D-tagatose-builds acid from16443

antibiotic resistance

  • @ref: 116495
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
11649535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole-
11649515688acetoin-
11649517234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68376alpha-mannosidase-3.2.1.24
68376beta-glucosidase-3.2.1.21
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
116495oxidase-
116495beta-galactosidase-3.2.1.23
116495alcohol dehydrogenase-1.1.1.1
116495gelatinase-
116495amylase-
116495DNase+
116495caseinase-3.4.21.50
116495catalase+1.11.1.6
116495tween esterase-
116495gamma-glutamyltransferase-2.3.2.2
116495lecithinase-
116495lipase-
116495lysine decarboxylase-4.1.1.18
116495ornithine decarboxylase-4.1.1.17
116495phenylalanine ammonia-lyase-4.3.1.24
116495tryptophan deaminase-
116495urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116495--++-+-+--+---------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUINOSorRHASACMELNO2N2
116495-------------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116495-------------------------------------------------

API LIST

@refDIMESCalpha MANDARLXYLRHAMDGRIBG1PTAG
116495----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116495---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationlatitudelongitudeisolation date
6937Activated sludgePortugalPRTEurope
67770Activated sludge of a treatment plant receiving chromium-contaminated wastewater from the tannery industry
67772Activated sludge of a treatment plant that receives wastewater from the tannery industry contaminated with chromiumPortugalPRTEurope1997Ribatejo, Alcanena39.4667-8.66667
116495Environment, Activated sludgePortugalPRTEurope2000

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Activated sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_38646.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1203;97_1419;98_3441;99_38646&stattab=map
  • Last taxonomy: Leucobacter aridicollis
  • 16S sequence: AJ781047
  • Sequence Identity:
  • Total samples: 1077
  • soil counts: 150
  • aquatic counts: 465
  • animal counts: 420
  • plant counts: 42

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69371Risk group (German classification)
677721
1164951Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67772
  • description: Leucobacter aridicollis partial 16S rRNA gene, type strain L9
  • accession: AJ781047
  • length: 1519
  • database: ena
  • NCBI tax ID: 283878

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leucobacter aridicollis L-9GCA_016758215scaffoldncbi283878
66792Leucobacter aridicollis strain DSM 17380283878.3wgspatric283878
66792Leucobacter aridicollis strain L-9283878.4wgspatric283878
66792Leucobacter aridicollis DSM 173802844811294draftimg283878
67770Leucobacter aridicollis DSM 17380GCA_013409595contigncbi283878

GC content

@refGC-contentmethod
693767.3
6777067.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno96.238no
gram-positiveyes88.719no
anaerobicno99.114no
aerobicyes88.718no
halophileno74.696no
spore-formingno94.041no
thermophileno99.748yes
glucose-utilyes73.986no
motileno84.165no
glucose-fermentno89.54no

External links

@ref: 6937

culture collection no.: DSM 17380, CIP 108388, LMG 22507, JCM 13321, IAM 15253, UCCCB9

straininfo link

  • @ref: 76800
  • straininfo: 131630

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392186Leucobacter iarius sp. nov., in the family Microbacteriaceae.Somvanshi VS, Lang E, Schumann P, Pukall R, Kroppenstedt RM, Ganguly S, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64683-02007Actinomycetales/*classification/genetics, Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Nematoda/*microbiology, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny26971343Leucobacter populi sp. nov. isolated from a symptomatic bark of Populus x euramericana canker.Fang W, Li X, Tan XM, Wang LF, Piao CG, Li YInt J Syst Evol Microbiol10.1099/ijsem.0.0010202016Actinobacteria/*classification/genetics/isolation & purification, Aminobutyrates/chemistry, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Bark/*microbiology, Populus/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny35939329Leucobacter chinensis sp. nov., with plant growth-promoting potential isolated from field soil after seven-years continuous maize cropping.Zhu J, Che J, Jiang X, Ma M, Guan D, Li L, Cao F, Zhao B, Kang Y, Zhao J, Kong D, Zhou Y, Ruan Z, Li JInt J Syst Evol Microbiol10.1099/ijsem.0.0054172022Actinobacteria, *Actinomycetales, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Triacetoneamine-N-Oxyl, *Zea maysTranscriptome

Reference

@idauthorscataloguedoi/urltitle
6937Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17380)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17380
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
33954Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6004
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67772Curators of the UCCCBhttps://ucccb.uc.pt/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68376Automatically annotated from API LIST
68382Automatically annotated from API zym
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76800Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131630.1StrainInfo: A central database for resolving microbial strain identifiers
116495Curators of the CIPCollection of Institut Pasteur (CIP 108388)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108388