Publications

4774

Abstract Xi.phi.ne.ma.to.bac'ter. Gr. neut. n. Xiphinema, ‐atos the genus name of the host organism; N.L. masc. n. bacter the equivalent of Gr. neut. n. baktron a rod; N.L. masc. n. Xiphinematobacter the rod‐shaped microbe associated with Xiphinema . Full‐grown cells are rod‐shaped with rounded ends, 0.7–1.0 × 2.1–3.2 μm ; however, cells in the J 1 (first juvenile) stage of nematode development have a wrinkled, pleomorphic shape. The longer entities usually consist of a mother cell from which a daughter cell is budding, giving rise to serial pairs typical of this bacterial genus. In thin sections cells have two or three membranes consisting of, from inside to outside, a cytoplasmic membrane, an electron‐dense outer membrane, and, in many individuals, a vacuolar membrane which is probably derived from the host cell membrane and which often shows discontinuities. No peptidoglycan layer is evident ; however, a periplasmic hexagonally arrayed monolayer of 10 nm protein units is sometimes present. Gram‐stain‐negative, nonmotile, and nonsporulating. DNA is often condensed at cell poles . Bacteria live as obligate cytoplasmic symbionts with maternal transmission in nematodes of the Xiphinema americanum group ( Nematoda, Longidoridae ), in which they are presumed to induce thelytokous ( mother‐to‐daughter ) parthenogenesis . DNA G + C content ( mol %): not determined. Type species : “ Candidatus Xiphinematobacter brevicolli ” Vandekerckhove, Willems, Gillis and Coomans 2000, 2203. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Xiphinematobacter is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Verrucomicrobiota / Terrimicrobiia / Terrimicrobiales / Chthoniobacteraceae / Candidatus Xiphinematobacter Candidatus Xiphinematobacter 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

Phy.to.plas'ma. Gr. masc. n.phytosa plant; Gr. neut. n.plasmasomething formed or molded, a form.Tenericutes / Mollicutes / Acholeplasmatales / incertae Sedis ‐ Family II / “Candidatus Phytoplasma”Phytoplasmas (Sears and Kirkpatrick, 1994) are wall‐less, nutritionally fastidious, phytopathogenic prokaryotes 0.2–0.8 µm in diameter that morphologically resemble members of theMollicutes. Sequencing of nearly full‐length PCR‐amplified 16S rRNA genes (Gundersen et al., 1994; Namba et al., 1993; Seemüller et al., 1994), combined with earlier studies (Kuske and Kirkpatrick, 1992b; Lim and Sears, 1989), provided the first comprehensive phylogeny of the organisms and showed that they constitute a unique, monophyletic clade within theMollicutes. These organisms are most closely related to members of the genusAcholeplasmawithin theAnaeroplasmaclade as defined by Weisburg et al. (1989). Sustained culture in cell‐free media has not yet been demonstrated for any phytoplasma. Their genome sizes have been estimated to range from 530 to 1350 kb, and the G+C content of phytoplasma DNA is about 23–30 mol%. The presence of a characteristic oligonucleotide sequence in the 16S rRNA gene, CAA GAY BAT KAT GTK TAG CYG GDC T, and standard codon usage indicate that phytoplasmas represent a distinct taxon for which the name “CandidatusPhytoplasma” has been adopted by specialists in the molecular biology and pathogenicity of these and similar phytopathogenic organisms (IRPCM Phytoplasma/Spiroplasma Working Team – Phytoplasma Taxonomy Group, 2004). At present, the designation “Candidatus” must still be used for new types.

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 Fri'tsche.a. N.L. fem. n. Fritschea named after Thomas R. Fritsche, an American physician and parasitologist, in honor of his contributions to our current knowledge on chlamydial diversity. Coccoid to rod‐shaped, nonmotile, obligately intracellular bacteria, up to 2.5 μm in length . Cells show a developmental cycle with morphologically distinct stages similar to those of the Chlamydiaceae . Organisms were found in whitefly and scale insects, but have not yet been obtained in cell culture. The genus is based on the description of “ Candidatus Fritschea bemisiae” and “ Candidatus Fritschea eriococci” (Everett et al., 2005; Thao et al., 2003) (Figure 1). Type species : “ Candidatus Fritschea bemisiae ” Everett, Thao, Horn, Dyszynski and Baumann 2005, 1585. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Fritschea is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Chlamydiota / Chlamydiia / Chlamydiales / Simkaniaceae / Candidatus Fritschea Candidatus Fritschea 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 Phlo.mo.bac.ter. Gr. n. phlomos bark; Gr. n. bakterion a small rod; M.L. neut. Phlomobacter rod in the bark. Filamentous bacteria occurring in the sieve tubes of phloem tissue of plants (Figures 1 and 2). The original description is from infected strawberry plants ( Fragaria × ananassa ) showing leaf marginal chlorosis and stunting in France (Nourrisseau et al., 1993). Like most other phloem‐restricted bacteria, Candidatus Phlomobacter fragariae has resisted in vitro cultivation. The mol % G + C of the DNA is : not determined. Type species : Candidatus Phlomobacter fragariae Zreik, Bové and Garnier 1998, 260. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Phlomobacter is: misspelling (and no standing) (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Pseudomonadota / Gammaproteobacteria / Enterobacterales / Enterobacteriaceae / Candidatus Phlomobacter Candidatus Phlomobacter 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 Thermoproteales (phylum Crenarchaeota ) populations are abundant in high-temperature (>70°C) environments of Yellowstone National Park (YNP) and are important in mediating the biogeochemical cycles of sulfur, arsenic, and carbon. The objectives of this study were to determine the specific physiological attributes of the isolate Pyrobaculum yellowstonensis strain WP30, which was obtained from an elemental sulfur sediment (Joseph's Coat Hot Spring [JCHS], 80°C, pH 6.1, 135 μM As) and relate this organism to geochemical processes occurring in situ . Strain WP30 is a chemoorganoheterotroph and requires elemental sulfur and/or arsenate as an electron acceptor. Growth in the presence of elemental sulfur and arsenate resulted in the formation of thioarsenates and polysulfides. The complete genome of this organism was sequenced (1.99 Mb, 58% G+C content), revealing numerous metabolic pathways for the degradation of carbohydrates, amino acids, and lipids. Multiple dimethyl sulfoxide-molybdopterin (DMSO-MPT) oxidoreductase genes, which are implicated in the reduction of sulfur and arsenic, were identified. Pathways for the de novo synthesis of nearly all required cofactors and metabolites were identified. The comparative genomics of P. yellowstonensis and the assembled metagenome sequence from JCHS showed that this organism is highly related (∼95% average nucleotide sequence identity) to in situ populations. The physiological attributes and metabolic capabilities of P. yellowstonensis provide an important foundation for developing an understanding of the distribution and function of these populations in YNP.