Allorhodoferax lacus


Citation

Formal styling
Allorhodoferax lacus 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:48720

Nomenclature

Rank
Species
Syllabication
la'cus
Etymology
L. gen. n. lacus, of a lake, referring to the habitat from which the type strain was isolated.
Nomenclatural type
NCBI Assembly: GCA_965194635.1
Reference strain
Strain sc|0038966: ZE-M1 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type strain is Allorhodoferax lacus ZE-M1 (GCA_965194635.1), isolated from 5 m depth from Lake Zurich, Switzerland (date: 2019-04-03), via high-throughput dilution to extinction cultivation. ZE-M1 has a genome size of 3.7 Mbp with a genomic GC content of 60.1%, contains 6 rRNA genes and 46 tRNAs. The genome is a high-quality draft consisting of 2 contigs. Genes for flagellar and pilus assembly were annotated. Pathways for cyanate and urea degradation, glycolate and methane/alkanesulfonate oxidation and the biosynthesis of all amino acids except for aspartate were predicted. Further, pathways for thiamine, riboflavin, NAD, coenzyme A, THF, cobalamin, and heme biosynthesis were identified. The closest cultivated relative is Curvibacter sp. AEP1-3 (GCF_002163715.1), with an average amino acid identity of 86.2% and average nucleotide identity of 81.9%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Rhodoferax_C; s__. 
Classification
Bacteria » Pseudomonadota » Betaproteobacteria » Burkholderiales » Comamonadaceae » Allorhodoferax » Allorhodoferax lacus
Parent
Allorhodoferax

Genomics

Accession
NCBI Assembly:GCA_965194635.1
Cultures
Strain sc|0038966
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 100.0%
  • Contamination: 0.0%
  • Quality: 100.0
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
509.0 ×
Source
Other features
  • G+C Content: 60.1%
  • Coding Density: 92.95%
  • Codon Table: 11
  • N50: 2,886,491 bp
  • Contigs: 2
  • Largest Contig: 2,886,491 bp
  • Assembly Length: 3,677,519 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 polished in Geneious 10 by repeated rounds of read mapping. Completeness and contamination were assessed with CheckM.
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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