Methylosemipumilus turicensisTs


Citation

Formal styling
Methylosemipumilus turicensisTs corrig. (ex Salcher et al., 2015) Salcher et al., 2019 (priority 2025)
Effective publication
Salcher et al., 2019
Original (not valid) publication
Salcher et al., 2015
Corrigendum
Salcher et al., 2019 from “Candidatus Methylopumilus turicensis” (sic)
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:y_q1qhwb (validated)
Canonical URL
https://seqco.de/i:44148

Nomenclature

Rank
Species
Syllabication
tu.ri.cen'sis
Etymology
N.L. masc. 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: GCF_000953015.1
Reference strain
Strain sc|0038981: MMS-10A-171 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type genome is Methylosemipumilus turicensis MMS-10A-171 (GCF_000953015.1), that was initially proposed as ‘Candidatus Methylopumilus turicensis’ in Salcher et. al. 2015 and later changed to Methylosemipumilus turicensis in Salcher et al. 2019. The strain was isolated by dilution-to-extinction cultivation from the water column of Lake Zurich, Switzerland. MMS-10A-171 has a genome size of 1.76 Mb with a genomic GC content of 44.52%, contains 6 rRNA genes and 40 tRNAs. The genome is complete, consisting of 1 circular chromosome. Methylosemipumilus turicensis MMS-10A-171 has a relatively small genome size (1.76 Mb) but not as small as Methylopumilus (1.3-1.4 Mb), which – together with improved genomic analyses – led to the reclassification to Methylosemipumilus. The genome contains genes encoding proteorhodopsins and the biosynthetic pathway for retinal biosynthesis. Pathways for methanol oxidation (Xox), the ribulose monophosphate (RuMP) cycle and the tetrahydromethanopterin (H4MPT) pathway for formaldehyde oxidation were predicted. The closest cultivated relatives are Methylotenera sp. L2L1 (GCF_000744605.1) with an average amino acid identity of 67.45% and average nucleotide identity of 70.55% and Methylovorus sp. MP688 (GCF_000183115.1) with an AAI of 69.37% and an ANI of 69.42%, while the genus Methylopumilus is more distantly related (AAI of 61.5-62.2% and ANI of 66.4-66.9%). 
Classification
Bacteria » Pseudomonadota » Betaproteobacteria » Nitrosomonadales » Methylophilaceae » Methylosemipumilus » Methylosemipumilus turicensisTs
Parent
Methylosemipumilus assigned in Salcher et al., 2019
Alternative placements
Pseudonyms
  • Candidatus Methylopumilus turicensis (Original, corrected name)

Genomics

Accession
NCBI Assembly:GCF_000953015.1
Cultures
Strain sc|0038981
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 100.0%
  • Contamination: 0.5%
  • Quality: 97.5
Ribosomal and transfer RNA genes
  • 2 16S rRNAs (up to 100.0%)
  • 2 23S rRNAs (up to 100.0%)
  • tRNAs for 20 amino acids
Sequencing depth
191.6 ×
Source
Other features
  • G+C Content: 44.5%
  • Coding Density: 92.01%
  • Codon Table: 11
  • N50: 1,754,988 bp
  • Contigs: 1
  • Largest Contig: 1,754,988 bp
  • Assembly Length: 1,754,988 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Genome of a culture with very slow growth and low yield. DNA was amplified by MDA (RepliPHI kit) prior to sequencing. Sequencing was done with Illuminia MiSeq (PE150), assembly was done with A5-miseq. The genome was manually curated to a circular chromosome in Geneious 7.1.7 by repeated rounds of read mapping, primer design for contig ends and low-coverage regions and sanger sequencing. 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
Over 1 year ago and claimed 7 months ago by Salcher, Michaela M
Submitted
7 months ago by Salcher, Michaela M
Curators
Validated
3 months ago by Palmer, Marike
Date of priority
2025-05-02 12:27 PM (UTC)

Publications
2

Citation Title
Salcher et al., 2019, The ISME Journal Evolution in action: habitat transition from sediment to the pelagial leads to genome streamlining in Methylophilaceae
Effective publication
Corrigendum
Assigned this taxon
Salcher et al., 2015, The ISME Journal The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign
Original (not valid) publication



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