Bathyarchaeum tardumTs


Citation

Formal styling
Bathyarchaeum tardumTs Khomyakova et al., 2023
Proposed in
Khomyakova et al., 2023
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:0qcnd580 (validated)
Cannonical URL
https://seqco.de/i:31303

Nomenclature

Rank
Species
Syllabication
tar'dum
Etymology
L. neut. adj. tardum, slow, referring to its slow growth
Nomenclatural type
INSDC Nucleotide: CP122380
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
According to our phylogenomic reconstruction based on 122 archaeal single copy conserved marker genes (Parks et al., 2018) Bathyarchaeum tardum is a part of BIN-L-1 genus-level lineage (Figure 1) which belongs to the BA1 family-level lineage and B26-1 order-level lineage according to GTDB (Parks et al., 2018). B26-1 group is formerly referred to as Bathy-8 (Yu et al., 2017). The phylogenetic position of Bathyarchaeum tardum revealed by 16S rRNA gene-based phylogenetic reconstruction agrees well with the phylogenomic data (Figure 2).
Description of Bathyarchaeum tardum
Cells are small, non-motile cocci, with a diameter of 0.4-0.7 μm. Occasionally forms chains of 3-5 cells covered by a common sheath. The cytoplasmic membrane is surrounded by an S-layer. Strictly anaerobic. Mesophilic. Grows at 10–45°C (optimum 37°C), at pH 6.0–10.0 (optimum 8.0) and at NaCl concentrations of 0–60 g l−1 (optimum 20 g l−1). Grows on 3,4-dimethoxybenzoic acid, vanillate in the presence of yeast extract, casamino acids or soytone. Does not utilize glucose, fructose, sucrose, lactate, pyruvate, lignin, chitin, peptone, tryptone, casein, cellulose, formate, methanol, benzoate, 3,4-dihydroxybenzoate, 2-methoxyphenol, 2-methoxybenzoate, molecular hydrogen and carbon monoxide. Dimethyl sulfoxide and nitrate stimulate growth, while oxygen, elemental sulfur, carbon monoxide and molecular hydrogen inhibit growth. Does not reduce sulfate, thiosulfate, antraquinone-2,6-disulfonate, selenate, selenite, arsenate, Fe(III)-citrate elemental sulfur, sulfite, nitrite or oxygen. Growth depends on addition of sterile natural sediment. The complete genome of strain M17C, available under the GenBank assembly accession number (CP122380Ts) is the designated nomenclatural type for the species and was recovered from an enrichment culture, cultivated on 3,4-dimethoxybenzoic acid and established from the anaerobic sediment of a coastal lake at the Taman Peninsula, Russian Federation. The genome has the size of 2.15 Mb and a G + C content of 38.1%. Completeness is estimated by CheckM at 98.28% with 0.934% contamination. Bathyarchaeum tardum is also presented by high-quality MAG M17C-73-01 (GCA_029762755.1; Genome size – 2139529bp, # of contigs – 12, completeness - 97.82%, contamination - 0.934%). Both MAGs have identical full-length 16S rRNA genes and ANI value between MAGs is 99.31%. With the other MAGs of the Bathyarchaeum genus, which were included in this genus based on our phylogenetic reconsideration (Figure 1), they have an ANI value no higher than 84.5%.
Classification
Archaea » “Bathyarchaeota” » Bathyarchaeia » Bathyarchaeales » Bathyarchaeaceae » Bathyarchaeum » Bathyarchaeum tardumTs
Parent
Bathyarchaeum

Genomics

Accession
INSDC Nucleotide:CP122380
Type
Enrichment Genome
Estimated Quality Metrics
  • Completeness: 98.28%
  • Contamination: 0.93%
  • Quality: 93.61
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 18 amino acids
Sequencing depth
450.0 ×
Source
Other features
  • G+C Content: 38.1%
  • Coding Density: 84.51%
  • Codon Table: 11
  • N50: 2,152,572 bp
  • Contigs: 1
  • Largest Contig: 2,152,572bp
  • Assembly Length: 2,152,572 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Completeness and contamination were evaluated using CheckM (Parks et al., 2015).
Annotation was made using PGAP (Tatusova et al., 2016).
tRNA elements were detected by tRNAscan-SE (Lowe and Eddy, 1997).

Automated checks
Complete
See additional details

Metadata

Outside links and data sources
Search sequences
Local history
Registered by
Merkel, Alexander 10 months ago
Submitted by
Merkel, Alexander 10 months ago
Curators
Endorsed by
Chuvochina, Maria 9 months ago
Validated by
Chuvochina, Maria 6 months ago

Publications
1

Citation Title
Khomyakova et al., 2023, Frontiers in Microbiology Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia
Proposed this name



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