St. John, Emily

A novel hyperthermophilic, heterotrophic and anaerobic archaeon, designated strain SLHALR2 T , was isolated from the ‘Cooking Pots’ hot springs at Hell’s Gate, Tikitere, New Zealand. During the exponential growth phase, cells of strain SLHALR2 T appear as long, thin rods to filaments, measuring 0.25–0.4 µm in width and 3.0–7.0 µm in length. Strain SLHALR2 T grows at temperatures ranging from 60 to 97 °C (optimum 80–85 °C), at pH values between 5.0 and 7.3 (optimum pH 6.0) and with 0–8 g l −1 sodium chloride concentration (optimum 0–1.0 g l −1 ). Elemental sulphur is reduced to hydrogen sulphide. Strain SLHALR2 T is an obligate organotroph capable of utilizing a variety of proteinaceous substrates and a limited range of sugars. Archaeal cell extracts improve growth but are not mandatory for growth. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicates that strain SLHALR2 T belongs to the genus Infirmifilum within the family Thermofilaceae , order Thermofilales (phylum Thermoproteota ). The strain shares 98.4–99% 16S rRNA gene sequence similarity with described Infirmifilum species. Despite this high level of 16S rRNA gene similarity with recently described Infirmifilum species, both average nucleotide identity (71–74%), average amino acid identity (67–75.5%) values and digital DNA–DNA hybridization values support the designation of strain SLHALR2 T as a distinct species within Infirmifilum . Based on phylogenomic analyses and the physiological characteristics of the novel isolate, strain SLHALR2 T is proposed as the type strain of a new species, Infirmifilum tikiterense sp. nov. (=OCM2026=UBOCC M-3571), and an emended description of the genus Infirmifilum is proposed.

Abstract Na.no.pu.sil'lus. Gr. masc. n. nânos, a dwarf; L. masc. adj. pusillus, very small; N.L. masc. n. Nanopusillus, a very small member of the Nanoarchaeota . The genus Candidatus Nanopusillus is comprised of small coccoid cells (∼100–400 nm) that live epibiotically on the surface of archaeal hosts. The first described species, Candidatus Nanopusillus acidilobi, is an anaerobic, hyperthermophilic acidophile whose best growth is observed at 82°C, pH 3.6, cultivated from a hot spring in Yellowstone National Park. Ca . Nanopusillus acidilobi cells associate with the Crenarchaeota host organism Acidilobus sp. 7A. Archaeal flagella (archaella) have been predicted from the genome sequence and shown to be expressed in the proteome. A second putative species, Candidatus Nanopusillus massiliensis, was recently reported from human dental plaque and associates with the methanogen Methanobrevibacter oralis . The genome consists of a single scaffold which is highly fragmented by spans of ambiguous nucleotides, with 16S rRNA gene fragments from Bacteria . Both species have small genomes (∼0.6 Mb) encoding few biosynthetic genes and no apparent ATP synthase complex genes, suggesting that the nanoarchaeotes rely on their host for the production of major cellular precursors. DNA G + C content (mol%) : 24 (genome analysis). Type species : Candidatus Nanopusillus acidilobi Wurch et al. 2016. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanopusillus is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Nanobdellota / Nanobdellia / Nanobdellales / Nanobdellaceae / Candidatus Nanopusillus The genus Candidatus Nanopusillus can also be recovered in the Genome Taxonomy Database (GTDB) as g__Nanopusillus (version v220) ** . GTDB classification: d__Archaea / p__Nanoarchaeota / c__Nanoarchaeia / o__Nanoarchaeales / f__Nanopusillaceae / g__Nanopusillus * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Na.no.clep'ta. Gr. masc. n. nânos, a dwarf; Gr. masc. n. kleptês, a thief; N.L. masc. n. Nanoclepta, a small thief, a small organism that steals from its host. The genus Candidatus Nanoclepta currently comprises a single species, Candidatus Nanoclepta minutus Ncl‐1, an anaerobic hyperthermophile (optimal growth observed from 80 to 85°C) cultivated from a New Zealand hot spring. Cells are ultra‐small cocci (∼200 nm) with archaeal flagella and are cultivated in near‐neutral pH conditions (pH ∼6.0). Like several other Nanoarchaeota , Ca . N. minutus cells are epibionts on the surface of a host from the Crenarchaeota . Although this symbiosis is obligate for Ca . N. minutus, the relationship is not required for the host, Zestosphaera tikiterensis NZ3 T , which can survive as a free‐living organism. Ca . N. minutus has a highly reduced genome (∼0.58 Mb) with minimal biosynthetic potential and no detected ATP synthase genes, and Ca . Nanoclepta cells likely rely on their host for many metabolic precursors. DNA G + C content (mol%) : 32.2 (genome analysis). Type species : Candidatus Nanoclepta minutus St. John et al. 2019a. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanoclepta is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Nanobdellota / Nanobdellia / Nanobdellales / Nanobdellaceae / Candidatus Nanoclepta The genus Candidatus Nanoclepta can also be recovered in the Genome Taxonomy Database (GTDB) as g__Nanoclepta (version v220) ** . GTDB classification: d__Archaea / p__Nanoarchaeota / c__Nanoarchaeia / o__Nanoarchaeales / f__Nanopusillaceae / g__Nanoclepta * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

AbstractTrace metals have been an important ingredient for life throughout Earth’s history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineageCaldarchaeales(syn.Aigarchaeota),Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) ofW. gerlachensisencodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show thatW. gerlachensispreferentially assimilates xylose. Phylogenetic analyses of 78 high-qualityWolframiiraptoraceaeMAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extantWolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.