Bergey's Manual of Systematics of Archaea and Bacteria

Abstract Ni.tro.so.cal.da'les. N.L. masc. n. Nitrosocaldus type genus of the order; ‐ ales ending to denote order; N.L. fem. pl. n. Nitrosocaldales the Nitrosocaldus order. Coccoid cells reproduce by binary fission. Thermophilic and neutrophilic. Obligately aerobic. Chemolithoautotrophic growth by ammonia oxidation to nitrite using CO 2 as carbon source. Some members can also use urea as an alternative source of energy for growth. Cell membrane is composed of isoprenoid tetraether lipids, including large amounts of acyclic and cyclized glycerol trialkyl glycerol tetraethers (GTGTs) and crenarchaeol (a unique glycerol dibiphytanyl glycerol tetraether (GDGT) containing one cyclohexane ring and four cyclopentane rings). Fully saturated and monounsaturated menaquinones with six isoprenoid units are present. They are globally distributed in various geothermal environments. Phylogenetic analyses of 16S rRNA and amoA gene sequences place the monophyletic order Ca . Nitrosocaldales as a basal lineage within the phylum Thaumarchaeota . This order can be distinguished from the closest order Nitrososphaerales by a lower mol% G + C content, a higher growth temperature (>60°C), and a higher relative abundance of GTGT. The order Ca . Nitrosocaldales is currently represented by a single family Ca . Nitrosocaldaceae. Type genus : Ca . Nitrosocaldus de la Torre, Walker, Ingalls, Könneke and Stahl 2008, 815. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the order Candidatus Nitrosocaldales is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Thermoproteati / Thermoproteota / incertae sedis / Candidatus Nitrosocaldales The order Candidatus Nitrosocaldales can also be recovered in the Genome Taxonomy Database (GTDB) as o__Nitrososphaerales (version v220) ** . GTDB classification: d__Archaea / p__Thermoproteota / c__Nitrososphaeria / o__Nitrososphaerales * 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 Ni.tro.so.cal'dus. N.L. adj. nitrosus nitrous; L. masc. adj. caldus hot; N.L. masc. n. Nitrosocaldus a nitrite producer at thermophilic growth temperatures. Thermophilic, neutrophilic, autotrophic, and aerobic ammonia‐oxidizing archaea. Urea can be used as a source of energy for growth. Cells fix CO 2 via a modified 3‐hydroxypropionate/4‐hydroxybutyrate carbon fixation pathway. Cells are irregular cocci between 0.65 and 0.75 microns in diameter. Cells reproduce by binary fission. Cell membrane lipids consist mainly of acyclic and cyclized glycerol trialkyl glycerol tetraethers (GTGTs) and glycerol dibiphytanyl glycerol tetraethers (GDGTs), with acyclic GTGT and crenarchaeol as the dominant components. Quinone systems include menaquinones with fully saturated and monounsaturated side chains that comprised six isoprenoid units. The members of the genus Ca . Nitrosocaldus can be found in neutral or slightly alkaline terrestrial geothermal environments at temperatures ranging from 65 to 85°C. Phylogenetic analysis on the basis of both 16S rRNA and amoA genes supports the monophyletic genus Ca . Nitrosocaldus within the family Ca . Nitrosocaldaceae. DNA G + C content (mol%) : 37.1. Type species : Ca . Nitrosocaldus yellowstonensis (Nitrosocaldus yellowstonii) de la Torre, Walker, Ingalls, Könneke and Stahl 2008, 815. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nitrosocaldus is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Thermoproteati / Thermoproteota / incertae sedis / Candidatus Nitrosocaldales / Candidatus Nitrosocaldaceae / Candidatus Nitrosocaldus The genus Candidatus Nitrosocaldus can also be recovered in the Genome Taxonomy Database (GTDB) as g__Nitrosocaldus (version v220) ** . GTDB classification: d__Archaea / p__Thermoproteota / c__Nitrososphaeria / o__Nitrososphaerales / f__Nitrosocaldaceae / g__Nitrosocaldus * 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 Cel.lu.lo.si.ly.ti.ca.ce'ae. N.L. neut. n. Cellulosilyticum a bacterial genus; N.L. fem. pl. n. Cellulosilyticaceae the Cellulosilyticum family. Slightly curved rod‐shaped cells . Gram‐positive cell‐wall structure but stain Gram‐negative. Terminal spores formed. Mesophilic, optimum growth temperature is approximately 40°C. Obligate anaerobic . No microaerophilic or aerobic growth occurs. Produce acetate, ethanol, and/or formate as the major end products, but not butyric or propionic acid. Hydrolyze cellulose and xylan and ferment cellobiose, but not ferment lactate and pyruvate. The predominant fatty acids are C 16:0 (27.1 %), C 14:0 (9.2 %), and iso‐C 16:0 (6.4%). Phylogenetically distant from the family Lachnospriaceae (Clostridum cluster XIVb), a member of the phylum Firmicutes, with less than 87.7% 16S rRNA similarity. Thus far, only one genus Cellulosilyticum is described. DNA G + C content (mol%) : 33–36. Type genus : Cellulosilyticum Cai and Dong 2010, 848 VP . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the family Cellulosilyticaceae is: synonym (last update, February 2025) * . Correct name: Lachnospiraceae LPSN classification: Bacteria / Bacillati / Bacillota / Clostridia / Eubacteriales / Lachnospiraceae The family Cellulosilyticaceae can also be recovered in the Genome Taxonomy Database (GTDB) as f__Cellulosilyticaceae (version v220) ** . GTDB classification: d__Bacteria / p__Bacillota_A / c__Clostridia / o__Lachnospirales / f__Cellulosilyticaceae * 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 Ni.tro.so.te'nu.is. N.L. adj. nitrosus, full of natron; here intended to mean nitrous; L. masc. adj. tenuis slender; N.L. masc. n. Candidatus Nitrosotenuis a slender nitrite producer. Candidatus Nitrosotenuis: a slender nitrite producer. Candidatus Nitrosotenuis is a genus of Thaumarchaeota that can be found widely distributed in soils, freshwater, hot springs, subsurface, and activated sludge. They may be rods or spheres and may or may not have flagella. Similar to other known and described Thaumarchaeota , Ca . Nitrosotenuis are aerobic chemolithautotrophs that use energy gained from the oxidation of ammonia to nitrite to fix carbon via the modified 3‐hydroxypropionate/4‐hydroxybutyrate carbon fixation pathway. At this time, no pure culture of Ca . Nitrosotenuis exists, but some of the six available enrichments have only a few rare contaminants. It remains to be demonstrated whether the remaining bacterial contaminants provide essential compounds to Ca . Nitrosotenuis. Enrichments of Ca . Nitrosotenuis are intolerant to high salinity (>0.3%), although they are phylogenetically placed within the group I.1a Thaumarchaeota ( Ca . Nitrosopumilales), which includes taxa that are widely distributed in the ocean. DNA G + C content (mol%) : 41.0–42.2. Type species : Candidatus Nitrosotenuis uzonensis . Lebedeva, Hatzenpichler, Pelletier, Schuster, Hauzmayer, Bulaev, Grigor'eva, Galushko, Schmid, Palatinszky, Le Paslier, Daims and Wagner 2013, 8. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nitrosotenuis is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Thermoproteati / Thermoproteota / Nitrososphaeria / Nitrosopumilales / Candidatus Nitrosotenuaceae / Candidatus Nitrosotenuis The genus Candidatus Nitrosotenuis can also be recovered in the Genome Taxonomy Database (GTDB) as g__Nitrosotenuis (version v220) ** . GTDB classification: d__Archaea / p__Thermoproteota / c__Nitrososphaeria / o__Nitrososphaerales / f__Nitrosopumilaceae / g__Nitrosotenuis * 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 Ni.tro.so.te.nu.a.ce'ae. N.L. adj nitrosus nitrous; L. adj. tenuis slender; ‐aceae ending to denote a family; N.L. fem. pl. n. Nitrosotenuaceae the Nitrosotenuis family. Candidatus Nitrosotenuaceae: A family of slender nitrite producers Candidatus Nitrosotenuaceae is a family of Thaumarchaeota that consists of a single genus, Ca . Nitrosotenuis, which can be found widely distributed in soils, freshwater, hot springs, the subsurface, and activated sludge. They may be rods or spheres and may or may not have flagella. Similar to other known and described Thaumarchaeota , Ca . Nitrosotenuaceae are aerobic chemolithautotrophs that use energy gained from the oxidation of ammonia to nitrite to fix carbon via modified 3‐hydroxypropionate/4‐hydroxybutyrate carbon fixation pathway. At this time, no pure culture of Ca . Nitrosotenuaceae exists, but some of the six available enrichments with members of the genus are almost pure. It remains to be demonstrated whether the remaining bacterial contaminants provide essential compounds to Ca . Nitrosotenuaceae. Enrichments of Ca . Nitrosotenuaceae are intolerant to high salinity (>0.3%), although they are phylogenetically related to the Group I.1a Thaumarchaeota ( Ca . Nitrosopumilaceae), which includes taxa that are widely distributed in the ocean. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the family Candidatus Nitrosotenuaceae is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Thermoproteati / Thermoproteota / Nitrososphaeria / Nitrosopumilales / Candidatus Nitrosotenuaceae The family Candidatus Nitrosotenuaceae can also be recovered in the Genome Taxonomy Database (GTDB) as f__Nitrosopumilaceae (version v220) ** . GTDB classification: d__Archaea / p__Thermoproteota / c__Nitrososphaeria / o__Nitrososphaerales / f__Nitrosopumilaceae * 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

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.

Abstract Ni.tro.so.ta.le.a'les. N.L. fem. n. Ca . Nitrosotalea type genus of the family; ‐ales ending to denote order; N.L. pl. n. Ca . Nitrosotaleales the Ca . Nitrosotalea order. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the order Nitrosotaleales is: correct name (last update, February 2025) * . LPSN classification: Archaea / Thermoproteati / Thermoproteota / Nitrososphaeria / Nitrosotaleales The order Nitrosotaleales can also be recovered in the Genome Taxonomy Database (GTDB) as o__Nitrososphaerales (version v220) ** . GTDB classification: d__Archaea / p__Thermoproteota / c__Nitrososphaeria / o__Nitrososphaerales * 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 Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Paracaedibacter is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Pseudomonadota / Alphaproteobacteria / Holosporales / Candidatus Paracaedibacteraceae / Candidatus Paracaedibacter Candidatus Paracaedibacter could not be recovered in GTDB ** . * 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

Apart from sharing the basic cellular features of otherBacteria, the cyanobacteria possess unique and diagnostic characteristics that will be briefly described here, but less extensively than in the 1989 edition ofBergey's Manual of Systematic Bacteriology. The cell wall in cyanobacteria is of a Gram‐negative type. Cell division in most unicellular and colonial cyanobacteria and some filamentous forms is by binary fission. Regarding cell exterior and motility, fimbriae (or pili) occur abundantly with diverse patterns in many cyanobacteria. Although not all thylakoids in cyanobacteria appear to be invaginations of the cytoplasmic membrane, there are orderly “attachment points” or “thylakoid centers” associated with the periphery of the cytoplasm or the cytoplasmic membrane. In the cytoplasm of cyanobacteria there are many other components and “inclusions”, most of which can be visualized readily using various preparative techniques for transmission electron microscopy. They include glycogen granules, cyanophycin granules, carboxysomes (polyhedral bodies), polyphosphate (volutin) granules, and gas vacuoles. Heterocysts, akinetes, and hormogonia are some of the specialized cells and differentiation in Cyanobacteria. The chief physiological/biochemical characteristic of cyanobacteria, distinguishing them from all other procaryotes, is the dual photosystem that allows the use of H2O as photoreductant with the consequent liberation of O2. Two courses for the delimitation of genera have been followed by cyanobacterial specialists: (a) to retain “small” genera or (b) to gather many species into fewer genera.Cyanobacteria / General Characteristics of the Cyanobacteria

Abstract Me.tha.no.bre.vi.bac'ter. M.L. neut. n. methanum methane; L. masc. adj. brevis short; M.L. masc. n. bacter equivalent of Gr. neut. n. bakterion rod, staff; M.L. masc. n. Methanobrevibacter short methane (‐producing) rod. Oval rods or cocci to short rods , usually occurring in pairs or chains; about 0.5–0.7 µm in width and 0.8–1.4 µm in length. Rarely, filaments are formed. Nonsporing, Gram‐positive. Cell walls are composed of pseudomurein . Nonmotile. Strict anaerobes. Optimum temperature, 37–40°C; maximum, ~45°C; minimum, ~30°C. The mol % G + C of the DNA is : 27.5–31.6. Type species : Methanobrevibacter ruminantium (Smith and Hungate 1958) Balch and Wolfe 1981, 216 (Effective publication: Balch and Wolfe in Balch, Fox, Magrum, Woese and Wolfe, 1979, 284) ( Methanobacterium ruminantium Smith and Hungate 1958, 717). Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Methanobrevibacter is: correct name (last update, February 2025) * . LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Methanobacteria / Methanobacteriales / Methanobacteriaceae / Methanobrevibacter The genus Methanobrevibacter can also be recovered in the Genome Taxonomy Database (GTDB) as g__Methanobrevibacter (version v220) ** . GTDB classification: d__Archaea / p__Methanobacteriota / c__Methanobacteria / o__Methanobacteriales / f__Methanobacteriaceae / g__Methanobrevibacter * 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