Publications

4691

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 Mag.ne'to.bac.te'ri.um. Gr. n. magnes magnet, comb. form magneto‐; Gr. n. bakterion a small rod; M.L. neut. n. Magnetobacterium a magnetic rod. Rod‐shaped, large, magnetic cells occurring in freshwater sediments. The original description is based on bacteria enriched from the littoral sediment of a freshwater lake in Southern Germany (Chiemsee); similar types of bacteria were also observed in sediments of other freshwater lakes and ponds in Southern Germany and Brazil. Counts of active bacteria in different vertical layers of Chiemsee sediment indicated that “ Candidatus M. bavaricum” is a typical gradient organism, particularly adapted to zones characterized by low levels of oxygen, where it reaches the highest abundance (Spring et al., 1993). A minor fraction of these bacteria was also found in the anoxic zone, whereas high concentrations of oxygen can apparently not be tolerated by this bacterium over longer periods of time. Type species : “ Candidatus Magnetobacterium bavaricum ” Spring, Amann, Ludwig, Schleifer, van Gemerden and Petersen 1993, 2398. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Magnetobacterium is: synonym (and no standing) (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Nitrospirota / Nitrospiria / Nitrospirales / Nitrospiraceae / Candidatus Magnetobacterium The genus Candidatus Magnetobacterium can also be recovered in the Genome Taxonomy Database (GTDB) as g__Magnetobacterium (version v220) ** . GTDB classification: d__Bacteria / p__Nitrospirota / c__Thermodesulfovibrionia / o__Thermodesulfovibrionales / f__Magnetobacteriaceae / g__Magnetobacterium * 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.

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.