Publications

4783

Abstract Bro.ca.di.a'les. N.L. fem. n. “ Candidatus Brocadia” type genus of the order; ‐ ales ending to denote an order; N.L. fem. pl. n. Brocadiales the order of “ Candidatus Brocadia”. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the order Candidatus Brocadiales is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Planctomycetota / Candidatus Brocadiia / Candidatus Brocadiales The order Candidatus Brocadiales can also be recovered in the Genome Taxonomy Database (GTDB) as o__Brocadiales (version v220) ** . GTDB classification: d__Bacteria / p__Planctomycetota / c__Brocadiia / o__Brocadiales * 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 Cla.vi.chla.my'di.a. L. n. clava a knotty branch, rough stick, cudgel, club; N.L. fem. n. Chlamydia taxonomic name of a bacterial genus; N.L. fem. n. Clavichlamydia a club Chlamydia (the morphology of the bacteria includes the characteristic head‐and‐tail cells that have been described earlier from salmonid fish suffering from epitheliocystis). Pleomorphic or elongated , nonmotile , obligate intracellular bacteria , up to 2 μ m in length . Cells show a developmental cycle with morphologically distinct stages and thrive inside a host vacuole . Organisms were found within gill lesions of fish and are differentiated from all other chlamydiae by the morphology of the proposed elementary bodies , which show a characteristic head‐and‐tail form (Figure 1). Members have not yet been obtained in cell culture. Type species : “ Candidatus Clavichlamydia salmonicola ” corrig. Karlsen, Nylund, Watanabe, Helvik, Nylund and Plarre 2008. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Clavichlamydia is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Chlamydiota / Chlamydiia / Chlamydiales / Chlamydiaceae / Candidatus Clavichlamydia The genus Candidatus Clavichlamydia can also be recovered in the Genome Taxonomy Database (GTDB) as g__Clavichlamydia (version v220) ** . GTDB classification: d__Bacteria / p__Chlamydiota / c__Chlamydiia / o__Chlamydiales / f__Chlamydiaceae / g__Clavichlamydia * 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.