Planktophila turicensis


Citation

Formal styling
Planktophila turicensis Salcher et al., 2025
Effective publication
Salcher et al., 2025
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:o5wsiwof (validated)
Canonical URL
https://seqco.de/i:49118

Nomenclature

Rank
Species
Syllabication
tu.ri.cen'sis
Etymology
N.L. neut. n. Turicum, the Latin name of Zurich; N.L. fem. adj. turicensis, referring to Turicum, the latin name of Zurich, pertaining to Lake Zurich, the isolation source of the type strain
Nomenclatural type
NCBI Assembly: GCA_965234405.1
Reference strain
Strain sc|0038793: ZE-9 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type species is Planktophila turicensis ZE-9 (GCA_965234405.1), isolated from 5 m depth from Lake Zurich, Switzerland (date: 2019-11-13), via high-throughput dilution to extinction cultivation. ZE-9 has a genome size of 1.4 Mbp with a genomic GC content of 48.5%, contains 3 rRNA genes and 39 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins. No genes for flagella or pilus assembly and chemotaxis were annotated. Pathways for taurine degradation and the biosynthesis of all amino acids except for histidine were predicted. Further, pathways for riboflavin, pyridoxal, coenzyme A, NAD, and menaquinone biosynthesis were identified. The closest cultivated relative is ‘Candidatus Planktophila sulfonica’ MMS-IA-56 (GCF_002288185.1), with an average nucleotide identity of 94.22%. Current GTDB classification (R220): d__Bacteria; p__Actinomycetota; c__Actinomycetia; o__Nanopelagicales; f__Nanopelagicaceae; g__Planktophila; s__. 
Classification
Bacteria » Actinomycetota » Actinomycetes » Nanopelagicales » Nanopelagicaceae » Planktophila » Planktophila turicensis
Parent
Planktophila

Genomics

Accession
NCBI Assembly:GCA_965234405.1
Cultures
Strain sc|0038793
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 99.16%
  • Contamination: 2.52%
  • Quality: 86.56
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 20 amino acids
Sequencing depth
645.2 ×
Source
Other features
  • G+C Content: 48.48%
  • Coding Density: 95.39%
  • Codon Table: 11
  • N50: 1,380,873 bp
  • Contigs: 1
  • Largest Contig: 1,380,873 bp
  • Assembly Length: 1,380,873 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Genome of a culture that was harvested by filtration on 0.22 µm filters; DNA was extracted with the Quiagen MagAttract HMW DNA kit. Sequencing was done with Illuminia Novaseq 6000, trimming of reads with BBMap v36.x, assembly with SPAdes v3.12.0. The genome was manually curated to a circular chromosome in Geneious 10 by repeated rounds of read mapping. Completeness and contamination were assessed with CheckM, but as the genome consists of a circular chromosome, it should be complete without any contamination.
Automated checks
Complete

Last modified 6 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
About 1 year ago by Salcher, Michaela M
Submitted
8 months ago by Salcher, Michaela M
Curators
Endorsed
6 months ago by Rodriguez-R, Luis M
Validated
3 months ago by Rodriguez-R, Luis M
Date of priority
2025-08-28 03:23 PM (UTC)

Publications
1

Citation Title
Salcher et al., 2025, Nature Communications Bringing the uncultivated microbial majority of freshwater ecosystems into culture
Effective publication



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