Fontibacterium subtropicum


Citation

Formal styling
Fontibacterium subtropicum Fernandes et al., 2025
Effective publication
Fernandes et al., 2025
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:gnukuc44 (validated)
Canonical URL
https://seqco.de/i:49877

Nomenclature

Rank
Species
Syllabication
sub.tro'pi.cum
Etymology
N.L. neut. adj. subtropicum, pertaining to subtropical zone, the isolation source of the MAG.
Nomenclatural type
NCBI Assembly: GCA_965235415.1
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type genome is Fontibacterium subtropicum N-SamH-20apr23-026 (GCA_965235415.1), a metagenome-assembled genome (MAG) assembled from 15 m depth from Lake Samsonvale, Australia (date: 2023-04-20). N-SamH-20apr23-026 has a genome size of 1.15 Mbp with a genomic GC content of 29.3%, contains 3 rRNA genes and 34 tRNAs. The genome is of high quality, consisting of 100 contigs, with a completeness of 100%, contamination of 1.2% and strain heterogeneity of 100% as assessed with checkM. The metagenome was assembled with FLYE from combined long-and short-read sequencing (Oxford Nanopore and Illumina NovaSeq). Metagenomic fragment recruitment of >600 samples from five continents indicate that the species is present mainly in subtropical lakes. The closest cultivated relatives are Fontibacterium commune, syn. ‘Candidatus Fonsibacter ubiquis’ LSUCC0530 (GCF_002688585.1; later reclassified to ‘Ca. Allofontibacter communis’), with an average amino acid identity of 88.13% and average nucleotide identity of 85.63% and another newly proposed species, Fontibacterium medardicus ME-17 (GCA_965235075.1), with an AAI of 90.92% and an ANI of 88.79%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Pelagibacterales; f__Pelagibacteraceae; g__Fonsibacter; s__Fonsibacter sp023257975.
Classification
Bacteria » Pseudomonadota » Alphaproteobacteria » Pelagibacterales » Pelagibacteraceae » Fontibacterium » Fontibacterium subtropicum
Parent
Fontibacterium

Genomics

Accession
NCBI Assembly:GCA_965235415.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 100.0%
  • Contamination: 1.2%
  • Quality: 94.0
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
59.3482 ×
Source
Other features
  • G+C Content: 29.3%
  • Coding Density: 93.13%
  • Codon Table: 11
  • N50: 284,470 bp
  • Contigs: 7
  • Largest Contig: 486,781 bp
  • Assembly Length: 1,155,633 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
This is a metagenome-assembled genome (MAG) that was assembled with FLYE v2.9.1-b1780 (settings: --nano-corr –meta –no-alt-contigs) from combined long- and short-read sequencing (Oxford Nanopore and Illumina NovaSeq). Contigs ≥3 kbp were used for hybrid binning (tetranucleotide frequencies and coverage data using cross-mapping of reads gained from the same lake, i.e., 2 samples in the case of Lake Samsonvale) using MaxBin-2.2.7, MetaBAT and MetaBAT2 and DAS Tool-1.1.3 to combine their predictions. Bins were manually curated and CheckM v1.1.3 was used to estimate bin completeness, contamination, and strain heterogeneity. rRNA genes were predicted with barrnap v0.9, tRNA genes were predicted with tRNAscan v1.4.
Automated checks
Complete

Last modified 4 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
8 months ago by Salcher, Michaela M
Submitted
3 months ago by Salcher, Michaela M
Curators
Validated
2 months ago by Rodriguez-R, Luis M
Date of priority
2025-08-28 03:13 PM (UTC)

Publications
1

Citation Title
Fernandes et al., 2025, Nature Microbiology Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium
Effective publication



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