Strain identifier

BacDive ID: 7453

Type strain: Yes

Species: Microbacterium lindanitolerans

Strain Designation: MNA2

Strain history: CCM 7585 <-- R. Lal; Univ. of Delhi, India; MNA2.

NCBI tax ID(s): 550448 (species)

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General

@ref: 16328

BacDive-ID: 7453

DSM-Number: 22422

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

description: Microbacterium lindanitolerans MNA2 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from hexachlorocyclohexane contaminated soil.

NCBI tax id

  • NCBI tax id: 550448
  • Matching level: species

strain history

@refhistory
16328<- R. Lal, Univ. Delhi, Dept. Zoology, India; MNA-2
67770CCM 7585 <-- R. Lal; Univ. of Delhi, India; MNA2.

doi: 10.13145/bacdive7453.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium lindanitolerans
  • full scientific name: Microbacterium lindanitolerans Lal et al. 2010

@ref: 16328

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium lindanitolerans

full scientific name: Microbacterium lindanitolerans Lal et al. 2010

strain designation: MNA2

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
29641positiverod-shapedno
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
21414Rape yellow (1021)10-14 daysISP 2
21414Zinc yellow (1018)10-14 daysISP 3
21414Rape yellow (1021)10-14 daysISP 4
21414Zinc yellow (1018)10-14 daysISP 5
21414Zinc yellow (1018)10-14 daysISP 7
21414Ziny yellow (1018)10-14 daysSuter with tyrosine
21414Zinc yellow (1018)10-14 daysSuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21414noISP 2
21414noISP 3
21414noISP 4
21414noISP 5
21414noISP 7
21414noSuter with tyrosine
21414noSuter without tyrosine

pigmentation

  • @ref: 29641
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcomposition
21414ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
21414ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
21414ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21414ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21414ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
21414Suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21414Suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
29641positivegrowth25-37mesophilic
29641positiveoptimum28-37mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29641positivegrowth06-11alkaliphile
29641positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

  • @ref: 29641
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.994

halophily

@refsaltgrowthtested relationconcentration
21414NaClpositivemaximum10 %
29641NaClpositivegrowth0-2 %
29641NaClpositiveoptimum0-2 %

observation

@refobservation
29641aggregates in chains
67770quinones: MK-12, MK-11, MK-13

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2141417234glucose+
2141422599arabinose+
2141417992sucrose+
2141418222xylose+
2141417268myo-inositol-
2141437684mannose+
2141428757fructose-
2141426546rhamnose+
2141416634raffinose-
2141462968cellulose-
2964117057cellobiose+carbon source
2964128757fructose+carbon source
2964128260galactose+carbon source
2964117234glucose+carbon source
2964117716lactose+carbon source
2964133942ribose+carbon source
2964130911sorbitol+carbon source
2964118222xylose+carbon source
296414853esculin+hydrolysis
2964117632nitrate+reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29641catalase+1.11.1.6
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-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382alkaline phosphatase-3.1.3.1
68379gelatinase-
68379urease+3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
21414-----++--+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21414-+/-+/--++/----+/-+/--++/-++++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
16328hexachlorocyclohexane contaminated soilIndiaINDAsia
67770Hexachlorocyclohexane-contaminated soilIndiaINDAsiaNorth India

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_156044.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_27915;97_45951;98_102879;99_156044&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: EU873539
  • Sequence Identity:
  • Total samples: 224
  • soil counts: 138
  • aquatic counts: 24
  • animal counts: 30
  • plant counts: 32

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
163281Risk group (German classification)
21414L1German classification

Sequence information

16S sequences

  • @ref: 16328
  • description: Microbacterium lindanitolerans strain MNA2 16S ribosomal RNA gene, partial sequence
  • accession: EU873539
  • length: 1289
  • database: ena
  • NCBI tax ID: 550448

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium lindanitolerans strain DSM 22422550448.3wgspatric550448
66792Microbacterium lindanitolerans DSM 224222811994985draftimg550448
67770Microbacterium lindanitolerans DSM 22422GCA_006788875contigncbi550448

GC content

@refGC-contentmethod
1632865.3high performance liquid chromatography (HPLC)
2964165.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno88no
gram-positiveyes91.118yes
anaerobicno99.504yes
halophileno65.558no
spore-formingno92.204no
glucose-utilyes89.117yes
thermophileno96.883yes
aerobicyes92.302yes
motileyes55.205yes
flagellatedno93.85yes
glucose-fermentno86.799no

External links

@ref: 16328

culture collection no.: DSM 22422, CCM 7585, JCM 30493

straininfo link

  • @ref: 76900
  • straininfo: 371118

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20023059Microbacterium lindanitolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil.Lal D, Gupta SK, Schumann P, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.017699-02009Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, DNA, Bacterial/genetics, Fatty Acids/metabolism, Hexachlorocyclohexane/*metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Soil Pollutants/*metabolismMetabolism
Phylogeny34232856Microbacterium chengjingii sp. nov. and Microbacterium fandaimingii sp. nov., isolated from bat faeces of Hipposideros and Rousettus species.Zhou J, Huang Y, Yang J, Lai XH, Jin D, Lu S, Pu J, Zhang S, Zhu W, Xu M, Huang Y, Liang J, Zheng H, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0048582021Animals, Bacterial Typing Techniques, Base Composition, China, Chiroptera/classification/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Microbacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16328Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22422)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22422
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
21414Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM22422.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29641Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2603028776041
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/
68379Automatically annotated from API Coryne
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)
76900Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID371118.1StrainInfo: A central database for resolving microbial strain identifiers