Pampinifervens diazotrophicumTs


Citation

Formal styling
Pampinifervens diazotrophicumTs Palmer et al., 2025
Effective publication
Palmer et al., 2025
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:54y7mje2 (validated)
Canonical URL
https://seqco.de/i:43940

Nomenclature

Rank
Species
Syllabication
di.a.zo.tro.phi'cum
Etymology
N.L. pref. diazo-, pertaining to dinitrogen; N.L. neut. adj. trophicum, feeding from Gr. masc. adj. trophikos; N.L. neut. adj. diazotrophicum, feeding on dinitrogen
Nomenclatural type
INSDC Nucleotide: CP117180.1
Reference strain
Strain sc|0040531: T-2 = JCM 35475 = DSM 116324 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
In addition to characteristics described for the genus, chemolithoautotrophic growth was observed using S0 as electron donor. Growth occurs in the absence of organic nitrogen sources, suggesting successful fixation of atmospheric dinitrogen. Growth occurs at 60-80 °C with an optimum at 70 °C, at pH 6.0-9.5 with an optimum at 8.5, at 0.2-10% oxygen with an optimum at 4%, and at sodium chloride concentrations ≤ 300 mM. Cells were 1.9-2.6 µm in length, and 0.3-0.5 µm in width, occurring singly. Colonies that are 0.5 mm in diameter, round, and entire in shape, and cream in color form after 7 days incubation under chemoautotrophic conditions. Major fatty acids are C20:1ω9c, C20:1ω7c, C18:0 and C20:0, while minor fatty acids include C16:0, C18:1ω7c and summed feature 8. Genomic G+C content of the type strain is 43.22%. Genealogical concordance and ANI support the novelty of this species, and phylogenomics and AAI places this species in the genus Pampinifervens gen. nov. The nomenclatural type for the species is the genome of strain T-2 (= JCM 35475=DSM 116324) from a white streamer community in Gumingquan (Drum Beating Spring) in the Rehai Geothermal Field, Tengchong County, China. The GenBank accession number for the complete genome of strain T-2 is CP117180 (BioProject: PRJNA659730, BioSample: SAMN15924605). 
Classification
Bacteria » Aquificota » Aquificia » Aquificales » Aquificaceae » Pampinifervens » Pampinifervens diazotrophicumTs
Parent
Pampinifervens ncbi

Genomics

Accession
INSDC Nucleotide:CP117180.1
Cultures
Strain sc|0040531
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 99.8%
  • Contamination: 0.0%
  • Quality: 99.8
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 21 amino acids
Sequencing depth
222.0 ×
Source
Other features
  • G+C Content: 43.3%
  • Coding Density: 96.19%
  • Codon Table: 11
  • N50: 1,692,950 bp
  • Contigs: 1
  • Largest Contig: 1,692,950 bp
  • Assembly Length: 1,692,950 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
A hybrid assembly was generated from ONT MinION sequence reads and Illumina sequence reads in SPAdes v. 3.14.1. The recovered genome was fully assembled to a single, closed replicon. Completeness and contamination estimates were done with CheckM v 1. The number and completeness of rRNA genes were determined with barrnap v. 0.9, and the number of tRNAs were determined with tRNAscan-SE v. 2.0. 
Automated checks
Complete

Last modified 14 days ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
Almost 2 years ago by Palmer, Marike
Submitted
Over 1 year ago by Palmer, Marike
Curators
Endorsed
Over 1 year ago by Rodriguez-R, Luis M
Validated
3 months ago by St. John, Emily
Date of priority
2025-08-26 03:49 PM (UTC)

Publications
1

Citation Title
Palmer et al., 2025, Systematic and Applied Microbiology Nitrogen fixation in Pampinifervens, a new species-rich genus of Aquificaceae that inhabits a wide pH range in terrestrial hot springs
Effective publication



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