Bergey's Manual of Systematics of Archaea and Bacteria

Abstract He.pat.in'co.la. Gr. neut. n. hêpar (gen. hêpatos) , liver; L. masc./fem. n. incola , inhabitant, dweller; N.L. masc. n. Hepatincola , a dweller of the liver. Pseudomonadota / Alphaproteobacteria / Rhodospirilalles / Candidatus Hepatincolaceae / Candidatus Hepatincola Candidatus Hepatincola is a genus of uncultured, obligately host‐associated bacteria originally discovered in the lumen of the midgut glands (hepatopancreas) of terrestrial isopods. In this niche, the bacteria exhibit a characteristic morphology: elongated rods with a stalk‐like appendage at one pole, which can be inserted between the microvilli of the midgut epithelium. All known members of the genus belong to two species ( Ca . Hepatincola porcellionum and a yet to be named Ca . Hepatincola sp.) associated with terrestrial isopods. However, closely related genera from the same family have been observed in numerous aquatic and terrestrial members of the Ecdysozoa (molting invertebrates). Ca . Hepatincola and closely related genera all have reduced genomes of about 1.3 Mb with low DNA G + C content ( c . 30%) and extremely limited biosynthetic capacities but rich in transporters to import essential nutrients and precursors from the environment. In line with its ecological niche (the host gut lumen, a nutrient‐rich environment) and genomic characteristics, Ca . Hepatincola is rather a nutrient scavenger than a nutrient provider for the host. Ca . Hepatincola was initially classified within the order Rickettsiales and later within the Holosporales , but recent phylogenomic analyses support its phylogenetic placement within the order Rhodospirillales . DNA G + C content (mol % ) : 30. Type species : Candidatus Hepatincola porcellionum Wang et al. (2004), CL1.

Abstract Krum.hol.zi.bac.te.ri.o'ta. N.L. neut. n. Krumholzibacterium , type genus of the type class of the phylum; L. neut. pl. n. suff. ‐ota , ending to denote a phylum; N.L. neut. pl. n. Krumholzibacteriota , the phylum of the class Krumholzibacteria. The phylum Candidatus Krumholzibacteriota was proposed to accommodate genomic assemblies of yet‐uncultured microorganisms. The type species, of the genus, Candidatus Krumholzibacterium zodletonense Zgenome0171 T was recovered from an anaerobic, sulfide‐ and sulfur‐rich spring in Southwestern Oklahoma, USA. The phylum comprises one described class, order, family, genus, and species. However, currently available genomes ( n  = 90) in GTDB (release 08‐RS214) are accommodated in 1 class, 6 orders, 8 families, 30 genera, and 58 species. Phylogenetically, the phylum is closely related to Gemmatimonadota and multiple phyla with no cultured representatives ( Ca . Edwardsbacteria, Ca . Eisenbacteria, Ca . Latescibacterota, Ca . Zixibacteria, 4572‐55, ARS69, GCA‐2686955, JAAXHH01, JABDJQ01, JAGLTZ01, JAGLYR01, TA06, TA06_A, and VGIX01); all of which are part of the FCB ( Fibrobacteres , Chlorobia , Bacteroidetes ) superphylum in the Gracilicutes clade. Candidatus Krumholzibacteriota genomes have mainly been recovered from marine, freshwater, engineered, and host‐associated ecosystems. The prevailing in‐situ conditions in sampled habitats, gene content analysis, and the use of predictive machine learning‐based approaches suggest a phylum‐wide preference for anaerobic conditions, mesophilic temperatures, circumneutral pH, and low salinities. Metabolically, the type species of the type genus of the phylum is predicted to be a fermentative anaerobe with preference for amino acids over sugars as substrates. Later studies indicate that some members of the phylum harbor respiratory capacities (dissimilatory sulfate reduction, dissimilatory sulfite reduction, iron‐reduction, and high‐affinity oxygen respiration with a few members possessing the potential for low‐affinity oxygen respiration), while others possess the machinery for anaerobic degradation of aromatic hydrocarbons. Finally, although all members of Candidatus Krumholzibacteriota remain uncultured, a representative of the phylum was enriched in a methane‐ and iron‐fed bioreactor inoculated with Bothnian Sea sediments. Type genus : Candidatus Krumholzibacterium Youssef et al. 2019, CL2.

Abstract Manc.ar.chae'um. L. masc. adj. mancus , crippled, maimed; N.L. neut. n. archaeum , an archaeon; N.L. neut. n. Mancarchaeum , a crippled archaeon, an archaeon with absence of many pathways in the genome. Microcaldota / Microcaldia / Candidatus Micrarchaeales / Candidatus Micrarchaeaceae / Candidatus Mancarchaeum The archaeon Candidatus Mancarchaeum was identified in a binary culture during the isolation of Cuniculiplasma divulgatum strain PM4. The culture was established with water saturated sediment sample from acidic stream flowing on Parys Mountain copper mine, Isle of Anglesey, UK. The proportion of genomic reads of Ca . Mancarchaeum in the binary culture was ca. 10%. Ca . Mancarchaeum is phylogenetically affiliated with members of the phylum Microcaldota , class Microcaldia , order Ca . Micrarchaeales, family Ca . Micrarchaeaceae. The cultivation experiments and analysis of the 952,257 bp genome suggest aerobic/microaerobic, organoheterotrophic (proteolytic/peptidolytic), acidophilic, and mesophilic lifestyle. The genome analysis showed the lack of complete central pathways and limited respiratory capacities, indicating reliance on the host, in that particular case, C. divulgatum PM4. The metagenomic analysis also suggested the lateral gene transfer events between the Ca . Mancarchaeum and host in situ . Ca . Mancarchaeum was found as a minor member of microbial community of Parys Mountain acid mine drainage stream. Further environmental distribution of representatives of this Candidatus genus showed preferences to habitats with low pHs and temperatures between 35 and 50°C. DNA G + C content (mol%) : 39.5 (genome sequence). Type species : Candidatus Mancarchaeum acidiphilum Golyshina et al. 2017, CL1.

Abstract Fer.men.ti.micr.ar.chae'um. L. gen. neut. n. fermenti , of a fermentation process; N.L. masc. adj. micros , small [probably better: micrus]; N.L. neut. n. archaeum , ancient one, archaeon; from Gr. adj. archaîos ‐a ‐on , ancient; N.L. neut. n. Fermentimicrarchaeum , a small archaeon performing fermentation processes. Microcaldota / Microcaldia / Candidatus Fermentimicrarchaeales / Candidatus Fermentimicrarchaeaceae / Candidatus Fermentimicrarchaeum The genus Candidatus Fermentimicrarchaeum was established based on complete genome sequence assembled from a freshwater lake sediment metagenome. Ca . Fermentimicrarchaeum is phylogenetically affiliated with the phylum Microcaldota (previously known as Candidatus Micrarchaeota) of the archaeal DPANN superphylum. Analysis of the 1.2 Mb genome of Ca . Fermentimicrarchaeum suggests that, contrary to the ARMAN group of Microcaldota and most DPANN members, this organism has complete glycolytic pathways and ATP generation mechanisms in substrate phosphorylation, the capacities to utilize some sugars and amino acids as substrates, and pathways for de novo nucleotide biosynthesis but lacks an aerobic respiratory chain. We suppose that Ca . Fermentimicrarchaeum is a free‐living scavenger rather than an obligate parasite or symbiont, and its functional role in lake sediments consists of the fermentation of low molecular weight organic compounds. 16S rRNA gene sequences and metagenome‐assembled genomes affiliated with Ca . Fermentimicrarchaeum were recovered from freshwater lake sediments and soils. DNA G + C content (mol%) : 46.4–48.5 (genome sequence). Type species : Candidatus Fermentimicrarchaeum limneticum Kadnikov et al. 2020, CL3.

Abstract Ba.be.lo'ta. N.L. fem. n. Babela , a Candidatus genus name; L. neut. pl. n. suff. ‐ ota , ending to denote a phylum; N.L. neut. pl. n. Babelota , the Candidatus Babela phylum. Candidatus Babelota is a phylum of strictly intracellular bacteria, currently divided into two class‐level groups and at least five orders based on 16S rRNA sequence analyses. However, all known biological isolates to date belong to the same order of the Babelales, within the Babelia class. Presently, four isolates representing three families have been described and maintained in laboratory cultures through the cultivation of their hosts, which are known to be amoeboid and flagellated protists. Genomic analysis of Ca . Babelota consistently reveals a profound reduction in metabolic capabilities, suggesting a phylum‐wide, conserved parasitic lifestyle. To date, all lineages covered by genomic data indicate that parasitism is a defining trait of this phylum. Ca . Babelota exhibits a cosmopolitan environmental distribution, with sequences detected across a spectrum of habitats including soil, freshwater, and saline or hypersaline water bodies. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the phylum Candidatus Babelota is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Bacteria / incertae sedis / Candidatus Babelota The phylum Candidatus Babelota can also be recovered in the Genome Taxonomy Database (GTDB) as p__Dependentiae (version v220) ** . GTDB classification: d__Bacteria / p__Dependentiae * 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 Natr.an.aer.o.vir.ga'ce.ae N.L. fem. n. Natranaerovirga, the type genus of the family, ‐ aceae ending to denote a family; N.L. fem. pl. n . Natranaerovirgaceae, the Natranaerovirga family. The family Natranaerovirgaceae includes obligately anaerobic fermentative bacteria from soda lakes. They are highly salt‐tolerant alkaliphiles utilizing carbohydrates as energy and carbon source. The family belongs to the order “Lachnospirales,” class Clostridia , and consists of a single genus Natranaerovirga . The family‐level status was established by phylogenomic analysis based on the Genome Taxonomy Database classification (GDTB). DNA G  +  C content (mol%) : 31.3–32.3 (whole‐genome sequence). Type genus : Natranaerovirga Sorokin et al. 2012, VL145. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the family Natranaerovirgaceae is: synonym (last update, February 2025) * . Correct name: Lachnospiraceae LPSN classification: Bacteria / Bacillati / Bacillota / Clostridia / Eubacteriales / Lachnospiraceae The family Natranaerovirgaceae can also be recovered in the Genome Taxonomy Database (GTDB) as f__DSM-24629 (version v220) ** . GTDB classification: d__Bacteria / p__Bacillota_A / c__Clostridia / o__Lachnospirales / f__DSM-24629 * 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.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

Abstract Thi.o.ha.lo.bac.ter.al'es N.L. masc. n. Thiohalobacter , the type genus of the order; L. fem. pl. n. suff. ‐ ales , ending to denote an order; N.L. fem. pl. n. Thiohalobacterales , the order of the genus Thiohalobacter . The order Thiohalobacterales accommodates obligately chemolithoautotrophic aerobic bacteria utilizing inorganic sulfur compounds as the energy source and assimilating CO 2 via the Calvin–Benson–Bassham cycle. The order is a deeply branching member of the Gammaproteobacteria and consists of two families Thiohalobacteraceae and Thiogranaceae, both of which include one genus. The order‐level status was established by phylogenomic analysis based on the Genome Taxonomy DataBase classification. Type genus : Thiohalobacter Sorokin et al. 2010 VP . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the order Thiohalobacterales is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Pseudomonadota / Gammaproteobacteria / Thiohalobacterales The order Thiohalobacterales can also be recovered in the Genome Taxonomy Database (GTDB) as o__Thiohalobacterales (version v220) ** . GTDB classification: d__Bacteria / p__Pseudomonadota / c__Gammaproteobacteria / o__Thiohalobacterales * 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 Thi.o.ha.lo.bac.ter.a.ce'ae N.L. masc. n. Thiohalobacter , the type genus of the family, ‐ aceae ending to denote a family; N.L. fem. pl. n. Thiohalobacteraceae the Thiohalobacter family. The family Thiohalobacteraceae consists of aerobic, chemolithoautotrophic, sulfur‐oxidizing bacteria from hypersaline salt lakes. They are moderately halophilic aerobic, bacteria utilizing reduced sulfur compounds as the energy source and assimilating CO 2 via the Calvin–Benson–Bassham cycle. The family is a member of the order Thiohalobacterales within the Gammaproteobacteria and consists of a single genus Thiohalobacter . The family‐level status was established by phylogenomic analysis based on the Genome Taxonomy DataBase classification. DNA G + C content (%) : 64.2 (genome sequence). Type genus : Thiohalobacter Sorokin et al. 2010 VP . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the family Thiohalobacteraceae is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Pseudomonadota / Gammaproteobacteria / Thiohalobacterales / Thiohalobacteraceae The family Thiohalobacteraceae can also be recovered in the Genome Taxonomy Database (GTDB) as f__Thiohalobacteraceae (version v220) ** . GTDB classification: d__Bacteria / p__Pseudomonadota / c__Gammaproteobacteria / o__Thiohalobacterales / f__Thiohalobacteraceae * 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