Bergey's Manual of Systematics of Archaea and Bacteria

Abstract Me.tha'no.thrix. N.L. neut. n. methanum methane; Gr. fem. n. thrix , hair; N.L. fem. n. Methanothrix , methane (‐producing) hair. Straight, rod‐shaped cells with flat ends, usually 0.8–1.3 μm wide by 2.0–6.0 μm long enclosed in a tubular sheath. Forms short (∼5–25 μm) to long (>150 μm) flexible chains of cells within the sheath. Nonmotile. Gram‐stain‐negative. Lipids contain myo ‐inositol, ethanolamine, and galactose as the polar head groups. Oxygen‐tolerant anaerobe. Organotrophic, splitting acetate into methane and CO 2 for energy generation. Some strains split formate into H 2 and CO 2 without producing methane. CO 2 can be reduced to methane in coculture with Geobacter spp. via direct interspecies electron transfer (DIET). Growth factors such as vitamins are stimulatory. Yeast extract is required, stimulatory or inhibitory, depending on the strain. NaCl is not required for growth. Optimal temperatures range from 34 to 37°C for mesophilic strains and 55 to 60°C for thermophilic strains; optimal pH range is 7.0–7.8. Gas vacuoles are generally found in thermophilic strains. Occur in both mesophilic and thermophilic anaerobic sludge digesters as well as anaerobic sediments. Synonymous with the genus Methanosaeta . DNA G + C content (mol%) : 51–61 (genome). Type species : Methanothrix soehngenii Huser et al. 1982, VL10. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Methanothrix is: correct name (last update, February 2025) * . LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Methanosarcinia / Methanosarcinales / Methanotrichaceae / Methanothrix The genus Methanothrix can also be recovered in the Genome Taxonomy Database (GTDB) as g__Methanothrix (version v220) ** . GTDB classification: d__Archaea / p__Halobacteriota / c__Methanosarcinia / o__Methanotrichales / f__Methanotrichaceae / g__Methanothrix * 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.sa.li.ni'co.la. Gr. masc. n. nanos dwarf; L. fem. pl. n. salinae saltworks; L. suff. –cola (from L. masc. or fem. n. incola ) inhabitant, dweller; N.L. masc. n. Nanosalinicola a dwarf‐sized organism inhabiting saltworks. The genus Candidatus Nanosalinicola corrig., originally described as Candidatus Nanosalinarum, was established based on a sequence from a metagenome recovered from the hypersaline Lake Tyrrell in Victoria, Australia. Ca . Nanosalinicola is phylogenetically affiliated with members of the Candidatus Nanohaloarchaeota branch ( Candidatus Nanosalina, Candidatus Nanopetraeus corrig., and Candidatus Haloredivivus) of the archaeal DPANN superphylum. On the basis of fluorescence in situ hybridization, cells are ∼0.6 μm in diameter. Analysis of the ∼1.22 Mb genome of Ca . Nanosalinicola J07AB56 with 56% DNA G + C suggests that the organism is an aerobic photoheterotroph. The high proportion of acidic amino acids of the predicted proteins suggests a “salt‐in” strategy for osmotic balance. Gene sequences affiliated with Ca . Nanosalinicola have also been recovered from coastal salterns in Australia and California, USA. DNA G + C content (mol%) : 56 (genome sequence). Type species : Not assigned. Genome sequence : AEIX00000000. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanosalinicola is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Candidatus Nanohalarchaeota / Candidatus Nanohaloarchaea / incertae sedis / incertae sedis / Candidatus Nanosalinicola Candidatus Nanosalinicola 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

Abstract Ha.lo.bo'num. Gr. masc. n. hals , halos salt; L. masc. adj. bonus good; N.L. neut. n. Halobonum a good salt organism. The genus Candidatus Halobonum with a single proposed species Candidatus Halobonum tyrrellense corrig. consists of extremely halophilic members of the haloarchaeal family Halorubraceae most closely related to the genus Halobaculum . The only isolate known was obtained from hypersaline surface waters of Lake Tyrrell, Victoria, Australia. In spite of the fact that a pure culture was isolated, Ca . Halobonum and Ca . Halobonum tyrrellense were described as Candidatus taxa. No cultures are currently available. Ca . Halobonum tyrrellense strain G22 was isolated on medium containing 235 g/l salt and with glycerol as the sole carbon source. Few phenotypic properties were reported. The genome size was estimated at 3,675,087 bp, with a DNA G + C content of 70.1 mol %. A putative sensory rhodopsin and a high number of ABC transporters and carbon metabolism genes were identified in the draft genome. 16S rRNA gene sequences affiliated with Ca . Halobonum were recovered from a hypersaline, ephemeral playa at the White Sands National Monument, New Mexico, USA, and from Chinese salt lakes and salterns. DNA G + C content (mol %) : 70.1 (genome sequence). Type species : Candidatus Halobonum tyrrellense. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Halobonum is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Halobacteria / Halobacteriales / Haloferacaceae / Candidatus Halobonum The genus Candidatus Halobonum can also be recovered in the Genome Taxonomy Database (GTDB) as g__Halobaculum (version v220) ** . GTDB classification: d__Archaea / p__Halobacteriota / c__Halobacteria / o__Halobacteriales / f__Haloferacaceae / g__Halobaculum * 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 Ha.lo.re.di.vi'vus. Gr. masc. n. hals , halos salt; L. masc. adj. redivivus renewed, renovated; N.L. masc. n. Haloredivivus a reconstructed salty organism. The genus Candidatus Haloredivivus was established based on a sequence of a single‐cell‐amplified genome recovered from a solar saltern pond of intermediate salinity in Spain. Ca . Haloredivivus is phylogenetically affiliated with members of the Candidatus Nanohaloarchaeota branch ( Candidatus Nanosalina, Candidatus Nanosalinicola corrig., and Candidatus Nanopetraeus corrig.) of the archaeal DPANN superphylum. Analysis of the ∼1.2 Mb genome of Ca . Haloredivivus with 42.1% G + C suggests that the organism leads a photoheterotrophic lifestyle and may be able to degrade different polysaccharides. The low median isoelectric point for the predicted proteins suggests a “salt‐in” strategy for osmotic balance. Gene sequences affiliated with Ca . Haloredivivus were recovered from a salt lake in Romania and from soda lakes in Siberia. DNA G + C content (mol%) : 42.0–42.1 (genome sequence). Type species : Not assigned. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Haloredivivus is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Candidatus Nanohalarchaeota / Candidatus Nanohaloarchaea / incertae sedis / incertae sedis / Candidatus Haloredivivus Candidatus Haloredivivus 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

Abstract Na.no.pe.trae'us. Gr. masc. n. nanos a dwarf; L. masc. adj. petraeus (from Gr. masc. adj. petraios ) living on or among the rocks; N.L. masc. n. Nanopetraeus small organism growing inside rocks. The originally proposed name Nanopetramus was corrected to Nanopetraeus . The genus Candidatus Nanopetraeus corrig. (originally named Candidatus Nanopetramus) was established based on a genome sequence found in the metagenome of halite endoliths sampled at Salar Grande in the northern Atacama Desert, Chile. A species name was not proposed. Candidatus Nanopetraeus is phylogenetically affiliated with members of the Ca . Nanohaloarchaeota branch ( Candidatus Haloredivivus, Candidatus Nanosalina, and Candidatus Nanosalinicola corrig.) of the archaeal DPANN superphylum. Analysis of the 1.1 Mb genome of Ca . Nanopetraeus SG9 with 46.4% DNA G + C suggests that the organism has a photoheterotrophic lifestyle, based on the presence of archaeal genes for carbohydrate metabolism and rhodopsin biosynthesis. The low median isoelectric point for the predicted proteins suggests a “salt‐in” strategy for osmotic balance. 16S rRNA gene sequences affiliated with Ca . Nanopetraeus were recovered from saltern ponds and hypersaline lakes worldwide. DNA G + C content (mol%) : 46.4 (metagenome‐assembled genome sequence). Type species : Not assigned. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanopetraeus is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Candidatus Nanohalarchaeota / incertae sedis / incertae sedis / incertae sedis / Candidatus Nanopetraeus Candidatus Nanopetraeus 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

Abstract Na.no.sa.li'na. Gr. masc. n. nanos dwarf; N.L. masc. adj. salinus salty; N.L. fem. n. Nanosalina a dwarf‐size salty organism. The genus Candidatus Nanosalina was established based on a sequence from a metagenome recovered from the hypersaline Lake Tyrrell in Victoria, Australia. Ca . Nanosalina is phylogenetically affiliated with members of the Candidatus Nanohaloarchaeota branch ( Candidatus Nanosalinicola corrig., Candidatus Nanopetraeus corrig., and Candidatus Haloredivivus) of the archaeal DPANN superphylum. On the basis of fluorescence in situ hybridization, cells are ∼0.6 μm in diameter. Analysis of the ∼1.23 Mb genome of Ca . Nanosalina J07AB43 with 43.5% DNA G + C suggests that the organism possesses an aerobic, photoheterotrophic lifestyle. The high proportion of acidic amino acids of the predicted proteins suggests a “salt‐in” strategy for osmotic balance. Gene sequences affiliated with Ca . Nanosalina have been recovered from coastal salterns in Australia and California, USA. DNA G + C content (mol%) : 43.5 (genome sequence). Type species : Not assigned. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanosalina is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Candidatus Nanohalarchaeota / Candidatus Nanohaloarchaea / Candidatus Nanosalinales / Candidatus Nanosalinaceae / Candidatus Nanosalina Candidatus Nanosalina 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

AbstractTheCampylobacterotais a novel phylum created from the reclassification of the proteobacterial classEpsilonproteobacteriaand orderDesulfurellales(Deltaproteobacteria). The phylum is organized according to phylogenies based on a concatenated alignment of 120 conserved protein marker sequences and the 16S rRNA gene. Like any phylogenetic inference, this road map is a hypothesis based on the data available at the time of writing and may be subject to change as new species are described, or other gene sequences considered. This road map incorporates relative evolutionary divergence to normalize subordinate ranks. It, therefore, includes a number of changes at the rank of order, family, and genus, which would otherwise not be affected by the merging of the former lineages.

Abstract Me.tha.no.hal'ar.chae.um N.L. neut. n. methanum methane; N.L. pref. methano ‐ pertaining to methane; Gr. masc. n. hals, halos salt; N.L. neut. n. archaeum (pertaining to archaios, ‐e, ‐on) ancient; N.L. neut. n. Methanohalarchaeum a salt‐loving archaeon forming methane. The candidate genus Ca . Methanohalarchaeum includes obligately anaerobic, extremely halophilic, neutrophilic, and moderately thermophilic methanogens with small coccoid cells producing methane by reduction of C 1 ‐methylated compounds using either H 2 or formate as electron donors. Amino acids or acetate is required as C‐source for assimilation. Core membrane lipids are represented by diphytanyl glycerol tetra‐ and diethers. Cells accumulate potassium as a compatible solute. They inhabit hypersaline lakes or salterns with neutral pH. The genus contains a single candidate species Ca . M. thermophilum, which is the type species. It is a member of the class Methanonatronarchaeia within a newly proposed phylum Halobacteriota (formerly part of the phylum Euryarchaeota ). DNA G + C content (mol%) : 35.4 (genome of the type strain). Type species : Ca . Methanohalarchaeum thermophilum Sorokin, Merkel, Abbas, Makarova, Rijpstra et al. 2018, 2206. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Methanohalarchaeum is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Methanonatronarchaeia / Methanonatronarchaeales / Methanonatronarchaeaceae / Candidatus Methanohalarchaeum The genus Candidatus Methanohalarchaeum can also be recovered in the Genome Taxonomy Database (GTDB) as g__Methanohalarchaeum (version v220) ** . GTDB classification: d__Archaea / p__Halobacteriota / c__Methanonatronarchaeia / o__Methanonatronarchaeales / f__Methanonatronarchaeaceae / g__Methanohalarchaeum * 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 Sci.sci.o.nel'la. N.L. fem. dim. n. Sciscionella arbitrary name formed from the acronym of the South China Sea Institute of Oceanology, SCISCIO, where taxonomic studies on this taxon were performed. The genus Sciscionella is classified as a member of the family Pseudonocardiaceae , order Pseudonocardiales , and in the class Actinobacteria . The member of this genus has a 16S rRNA sequence identity of less than 94% with the other members of the family Pseudonocardiaceae . In the phylogenetic tree based on 16S rRNA gene sequences, the single member of this genus, Sciscionella marina , forms a distant clade, closely related to the genera Haloechinothrix, Thermocrispum , and Yuhushiella . Cells are characterized with cell‐wall chemotype IV and phospholipid pattern type III sensu Lechevalier et al. 1977. The predominant respiratory quinone is MK‐9(H 4 ), and the fatty acid composition is dominated by saturated branched‐chain fatty acids, but not mycolic acids. Phenotypically, strains are aerobic and stain Gram‐positive. They could grow at 10–37°C, pH 6.0–8.0, and in the presence of up to 13% NaCl (w/v). The genus comprises one species, Sciscionella marina (the type species of the genus). DNA G + C content (mol%) : 68 (WGS). Type species : Sciscionella marina Tian, Zhi, Qiu, Zhang, Tang, Xu et al. 2009, 225 VP . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Sciscionella is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Bacillati / Actinomycetota / Actinomycetes / Pseudonocardiales / Pseudonocardiaceae / Sciscionella The genus Sciscionella can also be recovered in the Genome Taxonomy Database (GTDB) as g__Sciscionella (version v220) ** . GTDB classification: d__Bacteria / p__Actinomycetota / c__Actinomycetes / o__Mycobacteriales / f__Pseudonocardiaceae / g__Sciscionella * 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

Phy.to.plas'ma. Gr. neut. n.phyton, a plant; Gr. neut. n.plasmasomething formed or molded, a form; N.L. neut. n.Phytoplasma, a form from a plant.Tenericutes / Mollicutes / Acholeplasmatales / Incertae Sedis ‐ Family II /CandidatusPhytoplasmaThe generic name ‘CandidatusPhytoplasma’ has been adopted by specialists to refer to a monophyletic clade of wall‐less phytopathogenic bacteria affiliated with the orderAcholeplasmatalesin the classMollicutes. These small (<1 µm) pleomorphic cells occur within the nutritionally‐rich phloem sap and sieve elements of plants, and in the gut or hemolymph of insects that feed on plants. Sustained culture in cell‐free media has not yet been demonstrated for any phytoplasma, and a recent report of successful axenic culture remains to be independently replicated. Reference strains are maintained in plants by periodic graft inoculation. Sequence analysis of PCR‐amplified rDNA, plus considerations of the plant host range and vector species, provide a basis for phytoplasma strain identification and assignment to phylogenetic groups. Hundreds of plant species are susceptible to infection, with signs including discoloration, stunting, virescence, phyllody, proliferation of flowers or shoots, or sterility. The necessity for strict quarantine regulations to control the spread of phytoplasmas among important plants such as fruit trees, palms, and grapevines illustrates the importance of accurate identification and nomenclature for these organisms.