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Planktophila limneticaTs

Citation

Formal styling
Planktophila limneticaTs (ex Jezbera et al., 2009) Neuenschwander et al., 2018 (priority 2025)
Effective publication
Neuenschwander et al., 2018
Original (not valid) publication
Jezbera et al., 2009
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:kv6gij82 (validated)
Canonical URL
https://seqco.de/i:164

Nomenclature

Rank
Species
Syllabication
lim.ne.ti'ca
Etymology
N.L. fem. adj. limnetica, pertaining to lakes
Nomenclatural type
NCBI Assembly: GCF_002288365.1
Reference strain
Strain sc|0038937: MMS-VB-114 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
We propose the genome of strain MMS-VB-114 (GCF_002288365.1) as type for Planktophila limnetica and as type of the genus Planktophila as the original strain was never genome-sequenced. According to the previous description of a mixed culture (MWH-EgelM2-3.acI)(Jezbera et al., 2009) that has a 100% identical 16S rRNA gene sequences with strain MMS-VB-114, we propose the name Planktophila limnetica for strain MMS-VB-114 and make an amended description based on a complete genome. Represented by strain MMS-VB-114, which was isolated from Lake Zurich, Switzerland. Curved rods with lengths of 0.38±0.10 μm and diameters of 0.25±0.06 μm (see Table S3, Figure S1 in Neuenschwander et al. 2018). The initial pure culture was lost after a few propagations to fresh medium; no growing culture is available. The initial culture grew well in sterile lake water amended with pyruvate, urea, vitamins, and amino acids. P. limnetica MMS-VB-114 has a genome size of 1.33 Mbp and a genomic GC content of 45.0 %. It is auxotrophic for reduced sulfur sources and vitamins (B1, B5, B7), and possesses rhodopsins (see Table S7 in Neuenschwander et al. 2018). A complete genome is available at Genbank (GCF_002288365.1). Phylogenetic analyses of 476 concatenated protein sequences, 16S rRNA, 23S rRNA, and rhodopsin genes, as well as average nucleotide identities and protein similarities indicated the affiliation of the taxon to the family Nanopelagicaceae and the order Nanopelagicales.
Classification
Bacteria » Actinomycetota » Actinomycetes » Nanopelagicales » Nanopelagicaceae » Planktophila » Planktophila limneticaTs
Parent
Planktophila gtdb

Genomics

Accession
NCBI Assembly:GCF_002288365.1
Cultures
Strain sc|0038937
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 99.76%
  • Contamination: 0.32%
  • Quality: 98.16
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 19 amino acids
Sequencing depth
1000.0 ×
Source
Other features
  • G+C Content: 45.0%
  • Coding Density: 95.44%
  • Codon Table: 11
  • N50: 1,328,793 bp
  • Contigs: 1
  • Largest Contig: 1,328,793 bp
  • Assembly Length: 1,328,793 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Genome of a transient culture that was obtained by dilution-to-extinction cultivation. The DNA was amplified with a REPLI-g single cell kit and sequenced with a TruSeq PCR-free kit on an Illumina MiSeq instrument (v2 reagents, PE250). Reads were trimmed with trimmomatic-0.35.jar, assembled with SPAdes-3.7.0, and polished with Geneious. Completeness and contamination was assessed with CheckM2, but as the genome consists of a circular chromosome, it should be complete without any contamination.
Automated checks
Complete
See additional details
Last modified 7 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
Over 6 years ago and claimed 7 months ago by Salcher, Michaela M
Submitted
7 months ago by Salcher, Michaela M
Curators
Validated
6 months ago by Palmer, Marike
Date of priority
2025-04-30 03:20 PM (UTC)

Publications
3

Citation Title
Neuenschwander et al., 2018, The ISME Journal Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria
Effective publication
Karlov et al., 2011, Microbiology Microbial communities of water column of Lake Radok, East Antarctica, dominated by abundant actinobacterium “Candidatus Planktophila limnetica”
Jezbera et al., 2009, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 'Candidatus Planktophila limnetica', an actinobacterium representing one of the most numerically important taxa in freshwater bacterioplankton
Original (not valid) publication


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