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.

The Viking missions showed the martian soil to be lifeless and depleted in organic material and indicated the presence of one or more reactive oxidants. Here we report the presence of Mars-like soils in the extreme arid region of the Atacama Desert. Samples from this region had organic species only at trace levels and extremely low levels of culturable bacteria. Two samples from the extreme arid region were tested for DNA and none was recovered. Incubation experiments, patterned after the Viking labeled-release experiment but with separate biological and nonbiological isomers, show active decomposition of organic species in these soils by nonbiological processes.

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

In order to assess the effect of genome size and number of 16S rRNA genes (rDNAs) on the quantities of PCR-generated partial 16S rDNA fragments, equimolar amounts of DNA from pairs of different species for which these parameters are known were subjected to gene amplification. The experimentally determined ratio of PCR products obtained, as determined by image analysis of SYBR-Green I-stained amplification products, corresponded well with the predicted ratio calculated from the number of rrn genes per equimolar amounts of DNA in mixtures of Escherichia coli and ''Thermus thermophilus'' and of Pseudomonas aeruginosa and ''T. thermophilus.'' The values for the pair of Bacillus subtilis and ''T. thermophilus'' showed greater deviations from the predicted value. The dependence of the amount of 16S rDNA amplification product on these two parameters makes it impossible to quantify the number of species represented in 16S rDNA clone libraries of environmental samples as long as these two parameters are unknown for the species present.

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Strains ofThe genus Deinococcus includes the species Deinococcus radiodurans, Deinococcus proteolyticus, Deinococcus radiophilus, and Deinococcus radiopugnans. The species Deinococcus erythromyxa was also included in this genus as a species incertae sedis by Brooks and Murray (3). The rod-shaped organisms of the species Deinococcus grandis are very closely related to the species of the genus Deinococcus, but were classified in the genus Deinococcus primarily on the basis of morphology (36). Recently, the type strains of these species were subjected to a complete 16s ribosomal DNA (rDNA) sequence analysis, which resulted in the reclassification of Deinococcus grandis and Deinococcus erythromyxa (41). The species Deinococcus grandis, despite its rod-shaped morphology, falls within the radiation of the genus Deinococcus and for this reason was classified as Deinococcus grandis. The species Deinococcus erythromyxa was known by Brooks and Murray (3) to have characteristics that were different from those of the other species of Deinococcus, and subsequent studies confirmed its chemotaxonomic distinctiveness, which reinforced the need for reclassification of this species (12). The species Deinococcus erythromyxa has been found to be phylogenetically very closely related to the gram-positive species Kocuria rosea, but due to the low DNA-DNA hybridization values between the two species, Kocuria erythromyxa was maintained as a separate speciesThe species of the genus Deinococcus are strictly aerobic, have optimum growth temperatures in the range from 25 to 35"C, produce reddish colonies, generally stain gram positive, have ornithine in the peptidoglycan, lack teichoic acids, possess menaquinone 8 as the major respiratory quinone, and are (41).

The ionizing-radiation-resistant fractions of two soil bacterial communities were investigated by exposing an arid soil from the Sonoran Desert and a nonarid soil from a Louisiana forest to various doses of ionizing radiation using a 60 Co source. The numbers of surviving bacteria decreased as the dose of gamma radiation to which the soils were exposed increased. Bacterial isolates surviving doses of 30 kGy were recovered from the Sonoran Desert soil, while no isolates were recovered from the nonarid forest soil after exposure to doses greater than 13 kGy. The phylogenetic diversities of the surviving culturable bacteria were compared for the two soils using 16S rRNA gene sequence analysis. In addition to a bacterial population that was more resistant to higher doses of ionizing radiation, the diversity of the isolates was greater in the arid soil. The taxonomic diversity of the isolates recovered was found to decrease as the level of ionizing-radiation exposure increased. Bacterial isolates of the genera Deinococcus, Geodermatophilus, and Hymenobacter were still recovered from the arid soil after exposure to doses of 17 to 30 kGy. The recovery of large numbers of extremely ionizing-radiationresistant bacteria from an arid soil and not from a nonarid soil provides further ecological support for the hypothesis that the ionizing-radiation resistance phenotype is a consequence of the evolution of other DNA repair systems that protect cells against commonly encountered environmental stressors, such as desiccation. The diverse group of bacterial strains isolated from the arid soil sample included 60 Deinococcus strains, the characterization of which revealed nine novel species of this genus.Extreme ionizing-radiation resistance has been observed in several members of the domains Bacteria and Archaea. Of the genera containing ionizing-radiation-resistant organisms, Deinococcus and Rubrobacter show the highest levels of resistance, and all species of these genera have been shown to be