Podar, Mircea

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

“Cand. Nanosynbacter sp. HMT352” strain KC1 is an ectoparasitic saccharibacterium/TM7 that was co-isolated from a human saliva sample with its obligate bacterial host, Schaalia odontolytica . The genome of strain KC1 enables studies of the mechanisms and evolution of interspecies interactions and, for oral species, studies of their potential roles in health and disease.

Here, we report the draft, nearly complete genome sequence of the human oral actinobacterium Schaalia odontolytica strain ORNL0103, which was isolated in association with “ Candidatus Saccharibacteria” HMT352 strain ORNL0105. The genome was sequenced using a combination of Pacific Biosciences and Illumina platforms and encodes 1,948 proteins and 60 RNAs.

Na.no.ar.chae.a.ce'ae. N.L. neut. n. Nanoarchaeum type genus of the family; ‐ aceae ending to denote family; N.L. fem. pl. n. Nanoarchaeaceae the family of Nanoarchaeum . Euryarchaeota / Thermococci / Nanoarchaeales / Nanoarchaeaceae The “ Nanoarchaeaceae ” represent one of the two families within the “ Nanoarchaeales ”. They are extremely tiny cocci with reduced genomes. They are hyperthermophilic and anaerobic. They form a close association with their hosts and their growth depends on metabolic products of their host cells. Only one representative is cultivated in the laboratory.

The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota . Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, “ Candidatus Korarchaeum cryptofilum,” which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49%. Of the 1,617 predicted protein-coding genes, 1,382 (85%) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota . However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota . In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.

The hyperthermophile Nanoarchaeum equitans is an obligate symbiont growing in coculture with the crenarchaeon Ignicoccus . Ribosomal protein and rRNA-based phylogenies place its branching point early in the archaeal lineage, representing the new archaeal kingdom Nanoarchaeota. The N. equitans genome (490,885 base pairs) encodes the machinery for information processing and repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide biosyntheses. It is the smallest microbial genome sequenced to date, and also one of the most compact, with 95% of the DNA predicted to encode proteins or stable RNAs. Its limited biosynthetic and catabolic capacity indicates that N. equitans ' symbiotic relationship to Ignicoccus is parasitic, making it the only known archaeal parasite. Unlike the small genomes of bacterial parasites that are undergoing reductive evolution, N. equitans has few pseudogenes or extensive regions of noncoding DNA. This organism represents a basal archaeal lineage and has a highly reduced genome.