BioRepo | Biosample

Other Information

Key: 4439306413
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: 2024-07-02T10:14:08.110+00:00
CrawlId: 35
Extensions:
BasisOfRecord: MACHINE_OBSERVATION
IndividualCount: 8
OccurrenceStatus: PRESENT
TaxonKey: 11073618
KingdomKey: 3
PhylumKey: 111
ClassKey: 197
OrderKey: 1221
FamilyKey: 4891652
GenusKey: 3220030
SpeciesKey: 11073618
AcceptedTaxonKey: 11073618
ScientificName: Rhodopseudomonas palustris_C
AcceptedScientificName: Rhodopseudomonas palustris_C
Kingdom: Bacteria
Phylum: Proteobacteria
Order: Rhizobiales
Family: Xanthobacteraceae
Genus: Rhodopseudomonas
Species: Rhodopseudomonas palustris
GenericName: Rhodopseudomonas
SpecificEpithet: palustris
TaxonRank: SPECIES
TaxonomicStatus: ACCEPTED
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: 2024-07-02T10:14:08.110+00:00
License: http://creativecommons.org/publicdomain/zero/1.0/legalcode
OrganismQuantity: 8.0
OrganismQuantityType: individuals
IsSequenced: False
Identifiers:
- 0:
  - Identifier: V4R16_100
Media:
Facts:
Relations:
IsInCluster: False
SamplingProtocol: eDNA sampling from soil
GeodeticDatum: WGS84
Class: Alphaproteobacteria
CountryCode: LK
RecordedByIDs:
IdentifiedByIDs:
Country: Sri Lanka
GbifRegion: ASIA
PublishedByGbifRegion: ASIA
EventID: V4R16
Identifier: V4R16_100
GbifID: 4439306413
OccurrenceID: V4R16_100

Cell morphology:
- @ref: 121519
- Gram stain: negative
- Cell shape: rod-shaped
- Motility: yes

Culture medium:
- @ref: 121519
- Name: CIP Medium 69
- Growth: yes
- Link: https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=69
Culture temp:
- 0:
  - @ref: 121519
  - Growth: positive
  - Type: growth
  - Temperature: 30
- 1:
  - @ref: 121519
  - Growth: no
  - Type: growth
  - Temperature: 10
- 2:
  - @ref: 121519
  - Growth: no
  - Type: growth
  - Temperature: 41

Halophily:
- 0:
  - @ref: 121519
  - Salt: NaCl
  - Growth: positive
  - Tested relation: growth
  - Concentration: 0 %
- 1:
  - @ref: 121519
  - Salt: NaCl
  - Growth: no
  - Tested relation: growth
  - Concentration: 2 %
- 2:
  - @ref: 121519
  - Salt: NaCl
  - Growth: no
  - Tested relation: growth
  - Concentration: 4 %
- 3:
  - @ref: 121519
  - Salt: NaCl
  - Growth: no
  - Tested relation: growth
  - Concentration: 6 %
Metabolite utilization:
- 0:
  - @ref: 121519
  - Chebi-ID: 16947
  - Metabolite: citrate
  - Utilization activity: -
  - Kind of utilization tested: carbon source
- 1:
  - @ref: 121519
  - Chebi-ID: 4853
  - Metabolite: esculin
  - Utilization activity: -
  - Kind of utilization tested: hydrolysis
- 2:
  - @ref: 121519
  - Chebi-ID: 17632
  - Metabolite: nitrate
  - Utilization activity: -
  - Kind of utilization tested: reduction
- 3:
  - @ref: 121519
  - Chebi-ID: 16301
  - Metabolite: nitrite
  - Utilization activity: -
  - Kind of utilization tested: reduction
- 4:
  - @ref: 121519
  - Chebi-ID: 15792
  - Metabolite: malonate
  - Utilization activity: -
  - Kind of utilization tested: assimilation
Metabolite production:
- @ref: 121519
- Chebi-ID: 35581
- Metabolite: indole
- Production: no
Enzymes:
- 0:
  - @ref: 121519
  - Value: oxidase
  - Activity: +
- 1:
  - @ref: 121519
  - Value: beta-galactosidase
  - Activity: -
  - Ec: 3.2.1.23
- 2:
  - @ref: 121519
  - Value: alcohol dehydrogenase
  - Activity: -
  - Ec: 1.1.1.1
- 3:
  - @ref: 121519
  - Value: gelatinase
  - Activity: -
- 4:
  - @ref: 121519
  - Value: amylase
  - Activity: +
- 5:
  - @ref: 121519
  - Value: DNase
  - Activity: -
- 6:
  - @ref: 121519
  - Value: catalase
  - Activity: +
  - Ec: 1.11.1.6
- 7:
  - @ref: 121519
  - Value: tween esterase
  - Activity: +
- 8:
  - @ref: 121519
  - Value: lysine decarboxylase
  - Activity: -
  - Ec: 4.1.1.18
- 9:
  - @ref: 121519
  - Value: ornithine decarboxylase
  - Activity: -
  - Ec: 4.1.1.17
- 10:
  - @ref: 121519
  - Value: urease
  - Activity: +
  - Ec: 3.5.1.5
- 11:
  - @ref: 68382
  - Value: alkaline phosphatase
  - Activity: +
  - Ec: 3.1.3.1
- 12:
  - @ref: 68382
  - Value: esterase (C 4)
  - Activity: +
- 13:
  - @ref: 68382
  - Value: esterase lipase (C 8)
  - Activity: +
- 14:
  - @ref: 68382
  - Value: lipase (C 14)
  - Activity: -
- 15:
  - @ref: 68382
  - Value: leucine arylamidase
  - Activity: +
  - Ec: 3.4.11.1
- 16:
  - @ref: 68382
  - Value: valine arylamidase
  - Activity: -
- 17:
  - @ref: 68382
  - Value: cystine arylamidase
  - Activity: +
  - Ec: 3.4.11.3
- 18:
  - @ref: 68382
  - Value: trypsin
  - Activity: +
  - Ec: 3.4.21.4
- 19:
  - @ref: 68382
  - Value: alpha-chymotrypsin
  - Activity: -
  - Ec: 3.4.21.1
- 20:
  - @ref: 68382
  - Value: acid phosphatase
  - Activity: +
  - Ec: 3.1.3.2
- 21:
  - @ref: 68382
  - Value: naphthol-AS-BI-phosphohydrolase
  - Activity: -
- 22:
  - @ref: 68382
  - Value: alpha-galactosidase
  - Activity: -
  - Ec: 3.2.1.22
- 23:
  - @ref: 68382
  - Value: beta-galactosidase
  - Activity: -
  - Ec: 3.2.1.23
- 24:
  - @ref: 68382
  - Value: beta-glucuronidase
  - Activity: -
  - Ec: 3.2.1.31
- 25:
  - @ref: 68382
  - Value: alpha-glucosidase
  - Activity: -
  - Ec: 3.2.1.20
- 26:
  - @ref: 68382
  - Value: beta-glucosidase
  - Activity: -
  - Ec: 3.2.1.21
- 27:
  - @ref: 68382
  - Value: N-acetyl-beta-glucosaminidase
  - Activity: -
  - Ec: 3.2.1.52
- 28:
  - @ref: 68382
  - Value: alpha-mannosidase
  - Activity: -
  - Ec: 3.2.1.24
- 29:
  - @ref: 68382
  - Value: alpha-fucosidase
  - Activity: -
  - Ec: 3.2.1.51
API zym:
- @ref: 121519
- Control: -
- 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 biotype100:
- @ref: 121519
- GLU: -
- FRU: -
- GAL: +
- TRE: -
- MNE: -
- SBE: -
- MEL: -
- SAC: -
- RAF: -
- MTE: -
- MAL: -
- LAC: -
- LTE: -
- MbGa: -
- MaGa: -
- CEL: -
- GEN: -
- MbGu: -
- ESC: -
- RIB: -
- ARA: +
- XYL: -
- PLE: -
- RHA: -
- FUC: -
- MLZ: -
- DARL: -
- LARL: -
- XLT: -
- DUL: -
- TAG: -
- GLY: +
- INO: -
- MAN: -
- MTL: -
- TUR: -
- SOR: -
- ADO: -
- HBG: -
- LYX: -
- ERY: -
- MDG: -
- 3MDG: -
- SAT: +
- MUC: +
- LTAT: -
- DTAT: -
- MTAT: -
- DMLT: -
- LMLT: +
- CATE: -
- TATE: -
- TTE: -
- CIT: -
- GRT: -
- GAT: -
- 2KG: -
- 5KG: -
- TRY: -
- NAG: -
- GNT: -
- PAC: -
- PAT: -
- POBE: -
- QAT: -
- GTE: -
- MOBE: -
- BAT: -
- PPAT: -
- CMT: -
- TGE: -
- BET: -
- PCE: -
- ABT: -
- HIN: -
- LAT: -
- CAP: -
- CYT: -
- HIS: -
- SUC: -
- FUM: -
- GRE: -
- GYT: -
- AVT: -
- ETN: -
- TTN: -
- GLN: -
- ITA: -
- 3OBU: +
- APT: -
- GTT: -
- PRO: -
- DALA: -
- LALA: -
- SER: -
- MNT: -
- PROP: -
- TYR: -
- 2KT: -

Risk assessment:
- 0:
  - @ref: 20215
  - Biosafety level: 1
  - Biosafety level comment: Risk group
- 1:
  - @ref: 121519
  - Biosafety level: 1
  - Biosafety level comment: Risk group (French classification)

16S sequences:
- 0:
  - @ref: 20215
  - Description: Rhodopseudomonas palustris 16S rRNA, partial sequence
  - Accession: D12700
  - Length: 1319
  - Database: nuccore
  - NCBI tax ID: 1076
- 1:
  - @ref: 124043
  - Description: Rhodopseudomonas palustris gene for 16S rRNA, partial sequence, strain: ATCC 17001.
  - Accession: AB498815
  - Length: 1484
  - Database: nuccore
  - NCBI tax ID: 1076
- 2:
  - @ref: 124043
  - Description: Rhodopseudomonas palustris 16S rRNA, 16S-23S ribosomal RNA intergeic spacer, tRNA-Ile, tRNA-Ala, 23S rRNA, partial and complete sequence, strain: ATCC 17001.
  - Accession: AB498825
  - Length: 954
  - Database: nuccore
  - NCBI tax ID: 1076
- 3:
  - @ref: 124043
  - Description: Rhodopseudomonas palustris T 16S ribosomal RNA gene, partial sequence.
  - Accession: AF123087
  - Length: 1438
  - Database: nuccore
  - NCBI tax ID: 1076
- 4:
  - @ref: 124043
  - Description: Rhodopseudomonas palustris strain NCIMB8252 16S ribosomal RNA gene, partial sequence.
  - Accession: AF416662
  - Length: 1256
  - Database: nuccore
  - NCBI tax ID: 1076
- 5:
  - @ref: 124043
  - Description: Rhodopseudomonas palustris gene for 16S rRNA.
  - Accession: D25312
  - Length: 1412
  - Database: nuccore
  - NCBI tax ID: 1076

Lineage: cellular organisms; Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Nitrobacteraceae; Rhodopseudomonas
LineageEx:
- Taxon:
  - 0:
    - TaxId: 131567
    - ScientificName: cellular organisms
    - Rank: no rank
  - 1:
    - TaxId: 2
    - ScientificName: Bacteria
    - Rank: superkingdom
  - 2:
    - TaxId: 1224
    - ScientificName: Pseudomonadota
    - Rank: phylum
  - 3:
    - TaxId: 28211
    - ScientificName: Alphaproteobacteria
    - Rank: class
  - 4:
    - TaxId: 356
    - ScientificName: Hyphomicrobiales
    - Rank: order
  - 5:
    - TaxId: 41294
    - ScientificName: Nitrobacteraceae
    - Rank: family
  - 6:
    - TaxId: 1073
    - ScientificName: Rhodopseudomonas
    - 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

Safety information

Sequence information

Name and taxonomic classification