A new hierarchic classification structure for the taxa between the taxonomic levels of genus and class is proposed for the actinomycete line of descent as defined by analysis of small subunit (16s) rRNA and genes coding for this molecule (rDNA). While the traditional circumscription of a genus of the actinomycete subphylum is by and large in accord with the 16s rRNA/rDNA-based phylogenetic clustering of these organisms, most of the higher taxa proposed in the past do not take into account the phylogenetic clustering of genera. The rich chemical, morphological and physiological diversity of phylogenetically closely related genera makes the description of families and higher taxa so broad that they become meaningless for the description of the enclosed taxa. Here we present a classification system in which phylogenetically neighboring taxa at the genus level are clustered into families, suborders, orders, subclasses, and a class irrespective of those phenotypic characteristics on which the delineation of taxa has been based in the past. Rather than being based on a listing of a wide array of chemotaxonomic, morphological, and physiological properties, the delineation is based solely on 16s rDNA/rRNA sequence-based phylogenetic clustering and the presence of taxon-specific 16s rDNA/RNA signature nucleotides.In their publication "On the nature of global classification," Wheelis et al. (177) based the definition of higher taxa on the molecular level of universally homologous functions. This statement is derived from the high correlation of genealogical trees inferred from several such molecules, e.g., genes coding for 16s rRNA (16s rDNA) (179), 23s rDNA (96), elongation factors involved in the translation process, and the P-subunit of ATPase (97). The authors (177) stress that a basic requirement of a global classification is uniformity in methods and characteristics used in defining and ranking taxa. Nonhomologous characteristics, on the other hand, may be useful in confirming the molecular groupings. Application of this classification strategy led to the description of domains for the three highest taxa recognized today, the Archaea, Bacteria, and Eucarya Within the domain Bacteria, more than 15 lineages, which in phylogenetic uniqueness and ancestry are comparable to the archaeal kingdoms, have been identified. The taxonomic rank of kingdom has not yet been proposed for any of these lineages. The taxon class Proteobacteria has been proposed for a phylogenetically broad cluster of gram-negative genera, and several orders have been described for some of the phylogenetic lineages that emerged from the comparison of evolutionarily conserved macromolecules, e.g., Aquificales (19, Thermotogales (67), Verrucomicrobiales (173), and Planctomycetales (138). These phylogenetically coherent taxa are now used side by side with higher taxa that were described at the beginning of the pre-molecular era, i.e., before or around 1984. While the phylogenetic coherence of the division Firmacutes (53), the class Mollicutes, and the ord...

The genus Nocardiopsis was shown to be phylogenetically coherent and to represent a distinct lineage within the radiation of the order Actinomycetales. The closest relatives of the genus Nocardiopsis are members of the genera Actinomadura, Thermomonospora, Streptosporangium, and Microtetraspora. The intrageneric structure of the genus Nucardiupsis is shown to consist of a highly related species group containing Nucardiupsis dassonvillei, Nocardiopsis alborubida, and Nocardiopsis antarctica and a second group of less highly related species comprising Nocardiopsis alba subs p. alba, Nocardiopsis alba subs p. prasina, and Nocardiopsis listeri. Nocardiopsis lucentensis occupies a position intermediate between the two species groups. The results of a 16s ribosomal DNA sequence analysis are generally consistent with the available chemotaxonomic, phenotypic, and DNA-DNA hybridization data. The phylogenetic position and the morpho-and chemotaxonomic properties of Nocardiopsis species support the creation of a family for the genus Nocardiopsis, Nocardiopsaceae fam. nov.

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Dimethylsulfone is a major product of the chemical oxidation in the atmosphere of the principal biogenic sulfur gas, dimethylsulfide, but no studies have been reported on the mechanisms for its microbiological degradation. Three novel strains of bacteria have been isolated from enrichment cultures provided with dimethylsulfone as the only carbon and energy substrate. These are novel facultatively methylotrophic species of Hyphonmicrobium and Arthobacter, capable of growth on a range of one-carbon substrates. Cell-free extracts contained activities of enzymes necessary for a reductive/oxidative pathway for dimethylsulfone degradation: membrane-bound-dimethylsulfone and dimethylsulfoxide reductases, dimethylsulfide monooxygenase, and methanethiol oxidase. Enzymatic evidence is also presented for the subsequent oxidation of formaldehyde by formaldehyde and formate dehydrogenases in the Hyphomicrobium strain and by a dissimilatory ribulose monophosphate cycle in the Arthrobacter strains. The strains also grew on dimethylsulfoxide and dimethylsulfide, and dimethylsulfide-grown bacteria oxidized dimethylsulfide and dimethylsulfoxide but not dimethylsulfone. Formaldehyde assimilation was effected in the Hyphomicrobium strain by the serine pathway, but enzymes of the ribulose monophosphate cycle for formaldehyde assimilation were present in the Arthrobacter strains grown on dimethylsulfone. In contrast, one of the Arthrobacter strains was shown to switch to the serine pathway during growth on methanol. Growth yields on dimethylsulfone and formaldehyde were consistent with the occurrence of the serine pathway in Hyphomicrobium strain S1 and the ribulose monophosphate cycle in Arthrobacter strain TGA, and with the proposed reductive pathway for dimethylsulfone degradation in both.

Novel methylotrophic Arthrobacter and Hyphomicrobium species are described. Constitutive membrane-associated dimethylsulfone- and dimethylsulfoxide-reductases were found in Arthrobacter methylotrophus strain TGA and Hyphomicrobium sulfonivorans strain S1. Enzyme activities increased during growth with dimethylsulfone or dimethylsulfoxide, respectively, and different ratios of activity with different growth substrates indicated that they are separate enzymes. SDS-PAGE showed some membrane-associated polypeptides to be enhanced during growth with dimethylsulfone (54 kDa in H. sulfonivorans, 21-24 kDa, 54 kDa and 80 kDa in A. methylotrophus). Western blotting with anti-dimethylsulfoxide-reductase antibody showed cross-reaction with 54- and 21-kDa polypeptides in A. methylotrophus. All strains contained rhodanese and sulfur oxygenase after growth with dimethylsulfone. Sulfite was oxidized in the Arthrobacter species by APS reductase and sulfite dehydrogenase. H. sulfonivorans oxidized sulfite with APS reductase, which is unusual for an alpha-proteobacterium. The Arthrobacter species were distinguished from each other and from other Arthrobacter and Micrococcus species by 16S rRNA gene sequence analysis. The menaquinone and fatty acid profiles of the Arthrobacter species were similar. Their peptidoglycan structures were L-Lys- L-Ser- L-Thr- L-Ala for A. sulfonivorans and L-Lys- L-Ala(2-4) for A. methylotrophus. H. sulfonivorans exhibited gross morphology typical for Hyphomicrobium, but possessed helically twisted prosthecae. 16S rRNA gene sequence analysis showed it to be distinct from all the other Hyphomicrobium, Filomicrobium and Pedomicrobium species sequenced to date. Formal descriptions of the new species are given.