Verrucolacustris abundansTs


Citation

Formal styling
Verrucolacustris abundansTs Salcher et al., 2025
Effective publication
Salcher et al., 2025
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:opjv7zsc (validated)
Canonical URL
https://seqco.de/i:48694

Nomenclature

Rank
Species
Syllabication
a.bun'dans
Etymology
L. masc. part. adj. abundans, abundant; referring to high global abundances
Nomenclatural type
NCBI Assembly: GCA_965194535.1
Reference strain
Strain sc|0038970: MiH-22 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type strain is Verrucolacustris abundans MiH-22 (GCA_965194535.1), isolated from 15 m depth from Lake Milada, Czechia (date: 2019-10-15), via high-throughput dilution to extinction cultivation. MiH-22 has a genome size of 2.0 Mbp with a genomic GC content of 52.8%, contains 3 rRNA genes and 46 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins. No genes for flagellar assembly and chemotaxis were annotated. In contrast to other Methylacidiphilales members, no genes for C1 metabolism (methanotrophy) were identified. Pathways for assimilatory sulfate reduction and the biosynthesis of all amino acids except for methionine, histidine and tryptophan were predicted. Further, pathways for only three vitamins (thiamine, riboflavin, and biotin biosynthesis) were identified. The closest cultivated relative is Methylacidimicrobium cyclopophantes 3B_2 (GCF_902143385.2), with an average amino acid identity of 49.5% and average nucleotide identity of 62.8%. Current GTDB classification (R220): d__Bacteria; p__Verrucomicrobiota; c__Verrucomicrobiae; o__Methylacidiphilales; f__UBA3015; g__UBA3015; s__UBA3015 sp030054195.
Classification
Bacteria » Verrucomicrobiota » “Methylacidiphilae” » Methylacidiphilales » Verrucolacustridaceae » Verrucolacustris » Verrucolacustris abundansTs
Parent
Verrucolacustris

Genomics

Accession
NCBI Assembly:GCA_965194535.1
Cultures
Strain sc|0038970
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 90.6%
  • Contamination: 0.84%
  • Quality: 86.4
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
750.7 ×
Source
Other features
  • G+C Content: 52.8%
  • Coding Density: 94.06%
  • Codon Table: 11
  • N50: 2,045,411 bp
  • Contigs: 1
  • Largest Contig: 2,045,411 bp
  • Assembly Length: 2,045,411 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Genome of a culture with very slow growth and low yield. DNA was amplified by MDA prior to sequencing. 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
Over 1 year ago by Layoun, Paul
Submitted
7 months ago by Layoun, Paul
Curators
Endorsed
5 months ago by Rodriguez-R, Luis M
Validated
3 months ago by Valero Tebar, Juan
Date of priority
2025-08-28 03:27 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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