BioRepo | Biosample

Other Information

Key: 4439318107
DatasetKey: 7e9d3bc6-bb85-42a5-8826-fe2b27552e2c
PublishingOrgKey: 10edba3c-8fe0-4a8c-8767-312d0e2badb5
InstallationKey: f66ca88d-1f6a-49dc-b33b-32960faee57e
HostingOrganizationKey: fbca90e3-8aed-48b1-84e3-369afbd000ce
PublishingCountry: LK
Protocol: EML
LastCrawled: 2024-07-02T10:12:33.795+00:00
LastParsed: 2024-07-02T10:14:15.154+00:00
CrawlId: 35
Extensions:
BasisOfRecord: MACHINE_OBSERVATION
IndividualCount: 2
OccurrenceStatus: PRESENT
TaxonKey: 3224525
KingdomKey: 3
PhylumKey: 10813635
ClassKey: 10701801
OrderKey: 10877327
FamilyKey: 3838
GenusKey: 3224505
SpeciesKey: 3224525
AcceptedTaxonKey: 3224525
ScientificName: Micromonospora chalcea (Foulerton, 1905) Ørskov, 1923
AcceptedScientificName: Micromonospora chalcea (Foulerton, 1905) Ørskov, 1923
Kingdom: Bacteria
Phylum: Actinobacteriota
Order: Mycobacteriales
Family: Micromonosporaceae
Genus: Micromonospora
Species: Micromonospora chalcea
GenericName: Micromonospora
SpecificEpithet: chalcea
TaxonRank: SPECIES
TaxonomicStatus: ACCEPTED
IucnRedListCategory: NE
DecimalLatitude: 7.492081
DecimalLongitude: 80.348583
Continent: ASIA
Gadm:
- Level0:
  - Gid: LKA
  - Name: Sri Lanka
- Level1:
  - Gid: LKA.14_1
  - Name: Kurunegala
- Level2:
  - Gid: LKA.14.15_1
  - Name: Kurunegala
Year: 2022
Month: 2
Day: 8
EventDate: 2022-02-08
StartDayOfYear: 39
EndDayOfYear: 39
Issues:
LastInterpreted: 2024-07-02T10:14:15.154+00:00
License: http://creativecommons.org/publicdomain/zero/1.0/legalcode
OrganismQuantity: 2.0
OrganismQuantityType: individuals
IsSequenced: False
Identifiers:
- 0:
  - Identifier: V4R16_365
Media:
Facts:
Relations:
IsInCluster: False
SamplingProtocol: eDNA sampling from soil
GeodeticDatum: WGS84
Class: Actinomycetia
CountryCode: LK
RecordedByIDs:
IdentifiedByIDs:
Country: Sri Lanka
GbifRegion: ASIA
PublishedByGbifRegion: ASIA
EventID: V4R16
Identifier: V4R16_365
GbifID: 4439318107
OccurrenceID: V4R16_365

Colony morphology:
- 0:
  - @ref: 18738
  - Colony color: Red orange (2001)
  - Incubation period: 10-14 days
  - Medium used: ISP 2
- 1:
  - @ref: 18738
  - Colony color: Orange
  - Incubation period: 10-14 days
  - Medium used: ISP 3
- 2:
  - @ref: 18738
  - Colony color: Bright orange
  - Incubation period: 10-14 days
  - Medium used: ISP 4
- 3:
  - @ref: 18738
  - Colony color: Bright orange
  - Incubation period: 10-14 days
  - Medium used: ISP 5
- 4:
  - @ref: 18738
  - Colony color: Red orange (2001)
  - Incubation period: 10-14 days
  - Medium used: ISP 6
- 5:
  - @ref: 18738
  - Colony color: Bright orange
  - Incubation period: 10-14 days
  - Medium used: ISP 7
Multicellular morphology:
- 0:
  - @ref: 18738
  - Forms multicellular complex: no
  - Medium name: ISP 2
- 1:
  - @ref: 18738
  - Forms multicellular complex: no
  - Medium name: ISP 3
- 2:
  - @ref: 18738
  - Forms multicellular complex: no
  - Medium name: ISP 4
- 3:
  - @ref: 18738
  - Forms multicellular complex: yes
  - Complex name: Aerial Mycelium
  - Complex color: White
  - Medium name: ISP 5
- 4:
  - @ref: 18738
  - Forms multicellular complex: no
  - Medium name: ISP 6
- 5:
  - @ref: 18738
  - Forms multicellular complex: no
  - Medium name: ISP 7
Multimedia:
- @ref: 10697
- Multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43026.jpg
- Caption: Medium 65 28°C
- Intellectual property rights: © Leibniz-Institut DSMZ

Culture medium:
- 0:
  - @ref: 10697
  - Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  - Growth: yes
  - Link: https://mediadive.dsmz.de/medium/65
  - Composition: Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
- 1:
  - @ref: 18738
  - Name: ISP 2
  - Growth: yes
  - Composition: Name: 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
- 2:
  - @ref: 18738
  - Name: ISP 3
  - Growth: yes
  - Composition: Name: 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:
- 3:
  - @ref: 18738
  - Name: ISP 4
  - Growth: yes
  - Composition: Name: 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
- 4:
  - @ref: 18738
  - Name: ISP 5
  - Growth: yes
  - Composition: Name: 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
- 5:
  - @ref: 18738
  - Name: ISP 6
  - Growth: yes
  - Composition: Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
- 6:
  - @ref: 18738
  - Name: ISP 7
  - Growth: yes
  - Composition: Name: 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
- 7:
  - @ref: 10697
  - Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83)
  - Growth: yes
  - Link: https://mediadive.dsmz.de/medium/83
  - Composition: Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
Culture temp:
- 0:
  - @ref: 18738
  - Growth: positive
  - Type: optimum
  - Temperature: 28
- 1:
  - @ref: 10697
  - Growth: positive
  - Type: growth
  - Temperature: 28
- 2:
  - @ref: 67770
  - Growth: positive
  - Type: growth
  - Temperature: 28

Compound production:
- 0:
 - @ref: 10697
 - Compound: restriction endonuclease MchI
- 1:
 - @ref: 20216
 - Compound: Conversion of steroids
- 2:
 - @ref: 18738
 - Compound: Neorustmicin B
- 3:
 - @ref: 18738
 - Compound: Tetronolide
- 4:
 - @ref: 18738
 - Compound: Tetrocarcin E
- 5:
 - @ref: 18738
 - Compound: Tetrocarcin A
- 6:
 - @ref: 18738
 - Compound: Macquarimicin A
Halophily:
- @ref: 18738
- Salt: NaCl
- Growth: positive
- Tested relation: maximum
- Concentration: 2.5 %
Observation:
- @ref: 67770
- Observation: quinones: MK-10(H4), MK-10(H6)
Metabolite utilization:
- 0:
  - @ref: 68368
  - Chebi-ID: 5291
  - Metabolite: gelatin
  - Utilization activity: +
  - Kind of utilization tested: hydrolysis
- 1:
  - @ref: 68368
  - Chebi-ID: 27897
  - Metabolite: tryptophan
  - Utilization activity: -
  - Kind of utilization tested: energy source
- 2:
  - @ref: 68368
  - Chebi-ID: 16199
  - Metabolite: urea
  - Utilization activity: +
  - Kind of utilization tested: hydrolysis
- 3:
  - @ref: 68368
  - Chebi-ID: 16947
  - Metabolite: citrate
  - Utilization activity: +
  - Kind of utilization tested: assimilation
- 4:
  - @ref: 68368
  - Chebi-ID: 18257
  - Metabolite: ornithine
  - Utilization activity: +
  - Kind of utilization tested: degradation
- 5:
  - @ref: 68368
  - Chebi-ID: 25094
  - Metabolite: lysine
  - Utilization activity: +
  - Kind of utilization tested: degradation
- 6:
  - @ref: 68368
  - Chebi-ID: 29016
  - Metabolite: arginine
  - Utilization activity: +
  - Kind of utilization tested: hydrolysis
Metabolite production:
- 0:
  - @ref: 68368
  - Chebi-ID: 15688
  - Metabolite: acetoin
  - Production: yes
- 1:
  - @ref: 68368
  - Chebi-ID: 35581
  - Metabolite: indole
  - Production: no
- 2:
  - @ref: 68368
  - Chebi-ID: 16136
  - Metabolite: hydrogen sulfide
  - Production: no
Metabolite tests:
- 0:
  - @ref: 68368
  - Chebi-ID: 15688
  - Metabolite: acetoin
  - Voges-proskauer-test: +
- 1:
  - @ref: 68368
  - Chebi-ID: 35581
  - Metabolite: indole
  - Indole test: -
Enzymes:
- 0:
  - @ref: 68368
  - Value: gelatinase
  - Activity: +
- 1:
  - @ref: 68368
  - Value: tryptophan deaminase
  - Activity: -
  - Ec: 4.1.99.1
- 2:
  - @ref: 68368
  - Value: urease
  - Activity: +
  - Ec: 3.5.1.5
- 3:
  - @ref: 68368
  - Value: ornithine decarboxylase
  - Activity: +
  - Ec: 4.1.1.17
- 4:
  - @ref: 68368
  - Value: lysine decarboxylase
  - Activity: +
  - Ec: 4.1.1.18
- 5:
  - @ref: 68368
  - Value: arginine dihydrolase
  - Activity: +
  - Ec: 3.5.3.6
- 6:
  - @ref: 68368
  - Value: beta-galactosidase
  - Activity: -
  - Ec: 3.2.1.23
- 7:
  - @ref: 68382
  - Value: alkaline phosphatase
  - Activity: +
  - Ec: 3.1.3.1
- 8:
  - @ref: 68382
  - Value: esterase (C 4)
  - Activity: +
- 9:
  - @ref: 68382
  - Value: esterase lipase (C 8)
  - Activity: +
- 10:
  - @ref: 68382
  - Value: lipase (C 14)
  - Activity: -
- 11:
  - @ref: 68382
  - Value: leucine arylamidase
  - Activity: +
  - Ec: 3.4.11.1
- 12:
  - @ref: 68382
  - Value: valine arylamidase
  - Activity: +
- 13:
  - @ref: 68382
  - Value: cystine arylamidase
  - Activity: +
  - Ec: 3.4.11.3
- 14:
  - @ref: 68382
  - Value: trypsin
  - Activity: +
  - Ec: 3.4.21.4
- 15:
  - @ref: 68382
  - Value: alpha-chymotrypsin
  - Activity: +
  - Ec: 3.4.21.1
- 16:
  - @ref: 68382
  - Value: acid phosphatase
  - Activity: +
  - Ec: 3.1.3.2
- 17:
  - @ref: 68382
  - Value: naphthol-AS-BI-phosphohydrolase
  - Activity: +
- 18:
  - @ref: 68382
  - Value: alpha-galactosidase
  - Activity: +
  - Ec: 3.2.1.22
- 19:
  - @ref: 68382
  - Value: beta-galactosidase
  - Activity: +
  - Ec: 3.2.1.23
- 20:
  - @ref: 68382
  - Value: beta-glucuronidase
  - Activity: +
  - Ec: 3.2.1.31
- 21:
  - @ref: 68382
  - Value: alpha-glucosidase
  - Activity: +
  - Ec: 3.2.1.20
- 22:
  - @ref: 68382
  - Value: beta-glucosidase
  - Activity: +
  - Ec: 3.2.1.21
- 23:
  - @ref: 68382
  - Value: N-acetyl-beta-glucosaminidase
  - Activity: +
  - Ec: 3.2.1.52
- 24:
  - @ref: 68382
  - Value: alpha-mannosidase
  - Activity: -
  - Ec: 3.2.1.24
- 25:
  - @ref: 68382
  - Value: alpha-fucosidase
  - Activity: -
  - Ec: 3.2.1.51
API zym:
- @ref: 18738
- Alkaline phosphatase: +
- Esterase: +
- Esterase Lipase: +
- Lipase: -
- Leucine arylamidase: +
- Valine arylamidase: +
- Cystine arylamidase: +
- Trypsin: +
- Alpha- Chymotrypsin: +
- Acid phosphatase: +
- Naphthol-AS-BI-phosphohydrolase: +
- Alpha- Galactosidase: +
- Beta- Galactosidase: +
- Beta- Glucuronidase: +
- Alpha- Glucosidase: +
- Beta- Glucosidase: +
- N-acetyl-beta- glucosaminidase: +
- Alpha- Mannosidase: -
- Alpha- Fucosidase: -
API 20E:
- @ref: 18738
- ONPG: -
- ADH Arg: +
- LDC Lys: +
- ODC: +
- CIT: +
- H2S: -
- URE: +
- TDA Trp: -
- IND: -
- VP: +
- GEL: +

Taxonmaps:
- @ref: 69479
- File name: preview.99_1923.png
- Url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_404;97_1111;98_1509;99_1923&stattab=map
- Last taxonomy: Micromonospora
- 16S sequence: X92594
- Sequence Identity: None
- Total samples: 804
- Soil counts: 470
- Aquatic counts: 188
- Animal counts: 133
- Plant counts: 13

Risk assessment:
- 0:
  - @ref: 18738
  - Biosafety level: 1
- 1:
  - @ref: 10697
  - Biosafety level: 1
  - Biosafety level comment: Risk group (German classification)

16S sequences:
- 0:
  - @ref: 20218
  - Description: Micromonospora chalcea 16S ribosomal RNA gene sequence
  - Accession: U58531
  - Length: 1409
  - Database: nuccore
  - NCBI tax ID: 1874
- 1:
  - @ref: 10697
  - Description: M.chalcea 16S rRNA gene
  - Accession: X92594
  - Length: 1477
  - Database: nuccore
  - NCBI tax ID: 1874
- 2:
  - @ref: 10697
  - Description: Micromonospora chalcea strain 1464-217L 16S ribosomal RNA, partial sequence
  - Accession: NR_036795.1
  - Length: 1477
  - Database: nuccore
  - NCBI tax ID: 1874
- 3:
  - @ref: 67770
  - Description: Micromonospora chalcea gene for 16S ribosomal RNA, partial sequence
  - Accession: D85489
  - Length: 1459
  - Database: nuccore
  - NCBI tax ID: 1874
Genome sequences:
- 0:
  - @ref: 66792
  - Description: Micromonospora chalcea strain DSM 43026
  - Accession: 1874.5
  - Assembly level: wgs
  - Database: patric
  - NCBI tax ID: 1874
- 1:
  - @ref: 67770
  - Description: Micromonospora chalcea DSM 43026
  - Accession: GCA_002926165
  - Assembly level: contig
  - Database: ncbi
  - NCBI tax ID: 1874
GC content:
- 0:
  - @ref: 67770
  - GC-content: 71.9
  - Method: high performance liquid chromatography (HPLC)
- 1:
  - @ref: 67770
  - GC-content: 72.8
- 2:
  - @ref: 67770
  - GC-content: 72.79
  - Method: genome sequence analysis

Lineage: cellular organisms; Bacteria; Terrabacteria group; Actinomycetota; Actinomycetes; Micromonosporales; Micromonosporaceae; Micromonospora
LineageEx:
- Taxon:
  - 0:
    - TaxId: 131567
    - ScientificName: cellular organisms
    - Rank: no rank
  - 1:
    - TaxId: 2
    - ScientificName: Bacteria
    - Rank: superkingdom
  - 2:
    - TaxId: 1783272
    - ScientificName: Terrabacteria group
    - Rank: clade
  - 3:
    - TaxId: 201174
    - ScientificName: Actinomycetota
    - Rank: phylum
  - 4:
    - TaxId: 1760
    - ScientificName: Actinomycetes
    - Rank: class
  - 5:
    - TaxId: 85008
    - ScientificName: Micromonosporales
    - Rank: order
  - 6:
    - TaxId: 28056
    - ScientificName: Micromonosporaceae
    - Rank: family
  - 7:
    - TaxId: 1873
    - ScientificName: Micromonospora
    - Rank: genus

General Information

Sample Information

Other Information

General Information

Sample Information

Other Information

Occurence (geoference records)

Morphology

Culture and growth conditions

Physiology and metabolism

Isolation, sampling and environmental information

Safety information

Sequence information

Name and taxonomic classification